Starting phenix.real_space_refine
on Tue Feb  3 16:35:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hj0_52207/02_2026/9hj0_52207.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hj0_52207/02_2026/9hj0_52207.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hj0_52207/02_2026/9hj0_52207.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hj0_52207/02_2026/9hj0_52207.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hj0_52207/02_2026/9hj0_52207.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hj0_52207/02_2026/9hj0_52207.map"
  }
  resolution = 2.6
  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=   0.005
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      30      5.16       5
     C    3252      2.51       5
     N     853      2.21       5
     O     935      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 5070
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2233
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 273, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 258}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 2228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2228
          Classifications: {'peptide': 280}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 261}
          Chain breaks: 3
    Chain: "J"
      Number of atoms: 58
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 29
          Unusual residues: {'I74': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 29
          Unusual residues: {'I74': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "I"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "J"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C11AI74 J 401 " occ=0.51
      ... (56 atoms not shown)
      pdb=" O1 BI74 J 401 " occ=0.49
  Time building chain proxies: 1.37, per 1000 atoms: 0.27
  Number of scatterers: 5070
  At special positions: 0
  Unit cell: (84.132, 95.418, 66.69, 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      30     16.00
     O     935      8.00
     N     853      7.00
     C    3252      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.46
  Conformation dependent library (CDL) restraints added in 321.2 milliseconds
  

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1172

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      61.3% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'H' and resid 262 through 266
    Processing helix  chain 'H' and resid 271 through 275
    Processing helix  chain 'H' and resid 279 through 285
      removed outlier: 3.566A  pdb=" N   GLY H 285 " --> pdb=" O   GLN H 281 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.904A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 4
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 38
      removed outlier: 3.526A  pdb=" N   LEU I  19 " --> pdb=" O   SER I  15 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 49 through 70
      removed outlier: 3.670A  pdb=" N   VAL I  70 " --> pdb=" O   GLU I  66 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 76 through 91
    Processing helix  chain 'I' and resid 100 through 116
    Processing helix  chain 'I' and resid 121 through 128
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.781A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 178
    Processing helix  chain 'I' and resid 185 through 201
      removed outlier: 4.340A  pdb=" N   LYS I 189 " --> pdb=" O   GLU I 185 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   THR I 190 " --> pdb=" O   ILE I 186 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 225
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.616A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 242 through 262
    Processing helix  chain 'I' and resid 266 through 282
    Processing helix  chain 'J' and resid 56 through 67
    Processing helix  chain 'J' and resid 98 through 104
    Processing helix  chain 'J' and resid 110 through 131
    Processing helix  chain 'J' and resid 175 through 179
    Processing helix  chain 'J' and resid 180 through 185
    Processing helix  chain 'J' and resid 192 through 209
      removed outlier: 3.919A  pdb=" N   ALA J 198 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 239 through 243
    Processing helix  chain 'J' and resid 256 through 261
    Processing helix  chain 'J' and resid 265 through 276
    Processing helix  chain 'J' and resid 285 through 291
    Processing helix  chain 'J' and resid 292 through 297
      removed outlier: 3.938A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
    Processing sheet with id=AA1, first strand: chain 'J' and resid 16 through 20
      removed outlier: 6.532A  pdb=" N   VAL J  26 " --> pdb=" O   LEU J  18 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASP J  79 " --> pdb=" O   VAL J  90 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   LEU J  77 " --> pdb=" O   ASP J  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134

    267 hydrogen bonds defined for protein.
    750 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: 0.68

  Time building geometry restraints manager: 0.60 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: 1602
        1.34 -     1.46: 1182
        1.46 -     1.58: 2321
        1.58 -     1.70: 4
        1.70 -     1.81: 47
  Bond restraints: 5156
  Sorted by residual:
  bond pdb=" C3 AI74 J 401 "
       pdb=" N10AI74 J 401 "
    ideal  model  delta    sigma   weight residual
    1.335  1.490 -0.155 2.00e-02 2.50e+03 6.02e+01
  bond pdb=" C3 BI74 J 401 "
       pdb=" N10BI74 J 401 "
    ideal  model  delta    sigma   weight residual
    1.335  1.490 -0.155 2.00e-02 2.50e+03 5.98e+01
  bond pdb=" C26AI74 J 401 "
       pdb=" C8 AI74 J 401 "
    ideal  model  delta    sigma   weight residual
    1.497  1.603 -0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" C5 BI74 J 401 "
       pdb=" N18BI74 J 401 "
    ideal  model  delta    sigma   weight residual
    1.350  1.456 -0.106 2.00e-02 2.50e+03 2.80e+01
  bond pdb=" C26BI74 J 401 "
       pdb=" C8 BI74 J 401 "
    ideal  model  delta    sigma   weight residual
    1.497  1.601 -0.104 2.00e-02 2.50e+03 2.72e+01
  ... (remaining 5151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 6750
        1.38 -     2.76: 162
        2.76 -     4.14: 55
        4.14 -     5.52: 8
        5.52 -     6.90: 6
  Bond angle restraints: 6981
  Sorted by residual:
  angle pdb=" CB  GLU I 234 "
        pdb=" CG  GLU I 234 "
        pdb=" CD  GLU I 234 "
      ideal   model   delta    sigma   weight residual
     112.60  117.30   -4.70 1.70e+00 3.46e-01 7.63e+00
  angle pdb=" CG  ARG I 197 "
        pdb=" CD  ARG I 197 "
        pdb=" NE  ARG I 197 "
      ideal   model   delta    sigma   weight residual
     112.00  117.24   -5.24 2.20e+00 2.07e-01 5.67e+00
  angle pdb=" CB  MET J 189 "
        pdb=" CG  MET J 189 "
        pdb=" SD  MET J 189 "
      ideal   model   delta    sigma   weight residual
     112.70  119.60   -6.90 3.00e+00 1.11e-01 5.28e+00
  angle pdb=" C4 BI74 J 401 "
        pdb=" C3 BI74 J 401 "
        pdb=" N10BI74 J 401 "
      ideal   model   delta    sigma   weight residual
     126.93  120.09    6.84 3.00e+00 1.11e-01 5.20e+00
  angle pdb=" C4 AI74 J 401 "
        pdb=" C3 AI74 J 401 "
        pdb=" N10AI74 J 401 "
      ideal   model   delta    sigma   weight residual
     126.93  120.12    6.81 3.00e+00 1.11e-01 5.15e+00
  ... (remaining 6976 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 2694
       17.96 -    35.91: 304
       35.91 -    53.87: 80
       53.87 -    71.83: 19
       71.83 -    89.78: 10
  Dihedral angle restraints: 3107
    sinusoidal: 1298
      harmonic: 1809
  Sorted by residual:
  dihedral pdb=" CG  ARG I 197 "
           pdb=" CD  ARG I 197 "
           pdb=" NE  ARG I 197 "
           pdb=" CZ  ARG I 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.16   48.84     2      1.50e+01 4.44e-03 1.21e+01
  dihedral pdb=" CA  THR I 176 "
           pdb=" C   THR I 176 "
           pdb=" N   ARG I 177 "
           pdb=" CA  ARG I 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.94  -17.06     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  TYR I  91 "
           pdb=" C   TYR I  91 "
           pdb=" N   LEU I  92 "
           pdb=" CA  LEU I  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.04   16.96     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 3104 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 430
       0.027 -    0.054: 211
       0.054 -    0.081: 77
       0.081 -    0.108: 33
       0.108 -    0.135: 15
  Chirality restraints: 766
  Sorted by residual:
  chirality pdb=" CA  ILE J 255 "
            pdb=" N   ILE J 255 "
            pdb=" C   ILE J 255 "
            pdb=" CB  ILE J 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  TYR I  91 "
            pdb=" N   TYR I  91 "
            pdb=" C   TYR I  91 "
            pdb=" CB  TYR I  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  ILE J  74 "
            pdb=" N   ILE J  74 "
            pdb=" C   ILE J  74 "
            pdb=" CB  ILE J  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 763 not shown)

  Planarity restraints: 885
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR J 231 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO J 232 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO J 232 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO J 232 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN I 162 "   -0.024 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO I 163 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO I 163 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO I 163 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG I 165 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO I 166 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO I 166 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO I 166 "    0.020 5.00e-02 4.00e+02
  ... (remaining 882 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 239
        2.73 -     3.27: 5011
        3.27 -     3.81: 8833
        3.81 -     4.36: 10982
        4.36 -     4.90: 17776
  Nonbonded interactions: 42841
  Sorted by model distance:
  nonbonded pdb=" O1 AI74 J 401 "
            pdb=" O   HOH J 501 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   SER J 161 "
            pdb=" OH  TYR J 169 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" ND2 ASN I  27 "
            pdb=" OE2 GLU I  53 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" NE2 HIS I 161 "
            pdb=" O   HOH I 401 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   ASP J 155 "
            pdb=" O   HOH J 502 "
     model   vdw
     2.261 3.040
  ... (remaining 42836 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             0.410
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.930
  Find NCS groups from input model:        0.030
  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:9.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
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      :  0.006   0.155   5156  Z= 0.312
  Angle     :  0.602   6.896   6981  Z= 0.290
  Chirality :  0.040   0.135    766
  Planarity :  0.005   0.045    885
  Dihedral  : 17.086  89.782   1935
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.83 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 20.22 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.33), residues: 602
  helix:  1.57 (0.28), residues: 341
  sheet:  1.05 (1.10), residues: 14
  loop : -0.59 (0.36), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG I 197 
 TYR   0.015   0.001   TYR I  60 
 PHE   0.013   0.001   PHE I  71 
 TRP   0.013   0.001   TRP I  11 
 HIS   0.003   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00640 ( 5156)
  covalent geometry    : angle       0.60219 ( 6981)
  hydrogen bonds       : bond        0.15670 (  267)
  hydrogen bonds       : angle       6.55882 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.203 
Fit side-chains
REVERT: I  223 ARG cc_start: 0.7511 (ttt180) cc_final: 0.6966 (ttp80)
REVERT: J   13 GLU cc_start: 0.6724 (pt0) cc_final: 0.6183 (pt0)
REVERT: J   68 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6443 (mm-30)
REVERT: J   83 HIS cc_start: 0.4537 (OUTLIER) cc_final: 0.2852 (m90)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.7490
  time to fit residues: 77.9996
Evaluate side-chains
  100 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  219 SER
Chi-restraints excluded: chain I residue  244 CYS
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  137 ASP
Chi-restraints excluded: chain J residue  266 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0070
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 275 GLN
J  56 ASN
J 105 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.158249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.132873 restraints weight = 20343.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 3.32
r_work: 0.3282 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.0815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5156  Z= 0.105
  Angle     :  0.487   5.211   6981  Z= 0.251
  Chirality :  0.039   0.135    766
  Planarity :  0.004   0.035    885
  Dihedral  :  8.684  79.208    720
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.66 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 16.18 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.33), residues: 602
  helix:  2.01 (0.28), residues: 338
  sheet:  1.17 (0.93), residues: 14
  loop : -0.45 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I 197 
 TYR   0.013   0.001   TYR I  60 
 PHE   0.015   0.001   PHE I 110 
 TRP   0.007   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 5156)
  covalent geometry    : angle       0.48689 ( 6981)
  hydrogen bonds       : bond        0.04374 (  267)
  hydrogen bonds       : angle       4.83647 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.132 
Fit side-chains
REVERT: H  247 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7231 (mm-30)
REVERT: H  253 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7031 (mp)
REVERT: I  223 ARG cc_start: 0.7512 (ttt180) cc_final: 0.6974 (ttp80)
REVERT: I  250 ASP cc_start: 0.7209 (m-30) cc_final: 0.6927 (m-30)
REVERT: J   13 GLU cc_start: 0.6742 (pt0) cc_final: 0.6203 (pt0)
REVERT: J   22 GLN cc_start: 0.4102 (OUTLIER) cc_final: 0.3829 (pt0)
REVERT: J   68 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6506 (mm-30)
REVERT: J   83 HIS cc_start: 0.4610 (OUTLIER) cc_final: 0.3269 (m90)
REVERT: J   86 ASN cc_start: 0.5931 (m-40) cc_final: 0.5444 (m-40)
REVERT: J  153 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7385 (mt)
REVERT: J  171 HIS cc_start: 0.6896 (p-80) cc_final: 0.6645 (p90)
REVERT: J  188 ARG cc_start: 0.6564 (mmm160) cc_final: 0.6135 (mmm-85)
  outliers start: 23
  outliers final: 5
  residues processed: 106
  average time/residue: 0.5902
  time to fit residues: 64.6833
Evaluate side-chains
  102 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  247 GLU
Chi-restraints excluded: chain H residue  253 ILE
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain J residue   22 GLN
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  104 ASP
Chi-restraints excluded: chain J residue  119 LEU
Chi-restraints excluded: chain J residue  153 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 247 GLN
I 275 GLN
J 105 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.156379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.130845 restraints weight = 18899.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 3.17
r_work: 0.3297 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.0830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5156  Z= 0.134
  Angle     :  0.530   5.347   6981  Z= 0.268
  Chirality :  0.041   0.135    766
  Planarity :  0.005   0.036    885
  Dihedral  :  7.988  81.194    708
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.83 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 16.91 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.33), residues: 602
  helix:  1.95 (0.28), residues: 337
  sheet:  1.52 (1.01), residues: 14
  loop : -0.48 (0.36), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG I 197 
 TYR   0.016   0.001   TYR I  60 
 PHE   0.013   0.001   PHE I  71 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5156)
  covalent geometry    : angle       0.52956 ( 6981)
  hydrogen bonds       : bond        0.04901 (  267)
  hydrogen bonds       : angle       4.69692 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.122 
Fit side-chains
REVERT: H  247 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7222 (mm-30)
REVERT: H  253 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7007 (mp)
REVERT: I   33 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5907 (ttpm)
REVERT: I  223 ARG cc_start: 0.7474 (ttt180) cc_final: 0.6965 (ttp80)
REVERT: I  250 ASP cc_start: 0.7184 (m-30) cc_final: 0.6874 (m-30)
REVERT: J   13 GLU cc_start: 0.6724 (pt0) cc_final: 0.6171 (pt0)
REVERT: J   22 GLN cc_start: 0.4295 (OUTLIER) cc_final: 0.4009 (pt0)
REVERT: J   68 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6428 (mm-30)
REVERT: J   83 HIS cc_start: 0.4619 (OUTLIER) cc_final: 0.3241 (m90)
REVERT: J  105 ASN cc_start: 0.7536 (m-40) cc_final: 0.7030 (t0)
REVERT: J  153 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7498 (mt)
REVERT: J  171 HIS cc_start: 0.6966 (p-80) cc_final: 0.6693 (p90)
REVERT: J  188 ARG cc_start: 0.6555 (mmm160) cc_final: 0.6142 (mmm-85)
  outliers start: 21
  outliers final: 7
  residues processed: 101
  average time/residue: 0.4872
  time to fit residues: 50.8683
Evaluate side-chains
  102 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  247 GLU
Chi-restraints excluded: chain H residue  253 ILE
Chi-restraints excluded: chain I residue   33 LYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain J residue   22 GLN
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  104 ASP
Chi-restraints excluded: chain J residue  119 LEU
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 26 optimal weight:   30.0000
   chunk 50 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   chunk 39 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 57 optimal weight:    0.1980
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 247 GLN
I 275 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.129457 restraints weight = 19779.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.28
r_work: 0.3244 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.0914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5156  Z= 0.148
  Angle     :  0.551   6.033   6981  Z= 0.278
  Chirality :  0.042   0.134    766
  Planarity :  0.005   0.038    885
  Dihedral  :  8.015  80.904    708
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.99 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 15.62 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.33), residues: 602
  helix:  1.87 (0.28), residues: 337
  sheet:  1.75 (1.08), residues: 14
  loop : -0.54 (0.36), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG I 197 
 TYR   0.016   0.001   TYR I  60 
 PHE   0.015   0.002   PHE I  71 
 TRP   0.012   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5156)
  covalent geometry    : angle       0.55135 ( 6981)
  hydrogen bonds       : bond        0.05047 (  267)
  hydrogen bonds       : angle       4.64268 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.203 
Fit side-chains
REVERT: H  247 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7250 (mm-30)
REVERT: I   49 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6582 (mt-10)
REVERT: I  223 ARG cc_start: 0.7528 (ttt180) cc_final: 0.6975 (ttp80)
REVERT: J   13 GLU cc_start: 0.6842 (pt0) cc_final: 0.6232 (pt0)
REVERT: J   68 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6445 (mm-30)
REVERT: J   83 HIS cc_start: 0.4673 (OUTLIER) cc_final: 0.3238 (m90)
REVERT: J  105 ASN cc_start: 0.7677 (m-40) cc_final: 0.7181 (t0)
REVERT: J  153 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7504 (mt)
REVERT: J  188 ARG cc_start: 0.6723 (mmm160) cc_final: 0.6485 (mmm160)
  outliers start: 26
  outliers final: 13
  residues processed: 109
  average time/residue: 0.5688
  time to fit residues: 64.2051
Evaluate side-chains
  106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  247 GLU
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  141 GLU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  119 LEU
Chi-restraints excluded: chain J residue  137 ASP
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 247 GLN
I 275 GLN
J 171 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.154491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.129444 restraints weight = 15487.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.47
r_work: 0.3271 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.0994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5156  Z= 0.184
  Angle     :  0.606   6.309   6981  Z= 0.305
  Chirality :  0.044   0.139    766
  Planarity :  0.005   0.043    885
  Dihedral  :  8.147  81.845    708
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.16 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 16.73 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.33), residues: 602
  helix:  1.71 (0.28), residues: 336
  sheet:  1.78 (1.10), residues: 14
  loop : -0.63 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG I 197 
 TYR   0.018   0.002   TYR I  60 
 PHE   0.019   0.002   PHE I  71 
 TRP   0.014   0.002   TRP I  11 
 HIS   0.006   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 5156)
  covalent geometry    : angle       0.60559 ( 6981)
  hydrogen bonds       : bond        0.05525 (  267)
  hydrogen bonds       : angle       4.72691 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.204 
Fit side-chains
REVERT: H  247 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7155 (mm-30)
REVERT: I   33 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.5931 (ttpm)
REVERT: I   49 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6349 (mt-10)
REVERT: I   78 SER cc_start: 0.8451 (t) cc_final: 0.8237 (p)
REVERT: I  223 ARG cc_start: 0.7492 (ttt180) cc_final: 0.7000 (ttp80)
REVERT: J   13 GLU cc_start: 0.6798 (pt0) cc_final: 0.6179 (pt0)
REVERT: J   68 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6496 (mm-30)
REVERT: J   83 HIS cc_start: 0.4629 (OUTLIER) cc_final: 0.3272 (m90)
REVERT: J  153 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7505 (mt)
  outliers start: 25
  outliers final: 12
  residues processed: 109
  average time/residue: 0.6075
  time to fit residues: 68.5774
Evaluate side-chains
  108 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  247 GLU
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   33 LYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  141 GLU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  137 ASP
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 15 optimal weight:    0.4980
   chunk 57 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
I 153 GLN
I 155 ASN
I 247 GLN
I 275 GLN
J 105 ASN
J 171 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.155495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.130216 restraints weight = 20514.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 3.47
r_work: 0.3233 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5156  Z= 0.154
  Angle     :  0.573   7.258   6981  Z= 0.289
  Chirality :  0.042   0.137    766
  Planarity :  0.005   0.043    885
  Dihedral  :  8.072  81.040    708
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.49 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 17.65 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.33), residues: 602
  helix:  1.77 (0.28), residues: 336
  sheet:  1.87 (1.09), residues: 14
  loop : -0.62 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG I 197 
 TYR   0.016   0.002   TYR I  60 
 PHE   0.018   0.002   PHE I  71 
 TRP   0.013   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5156)
  covalent geometry    : angle       0.57307 ( 6981)
  hydrogen bonds       : bond        0.05067 (  267)
  hydrogen bonds       : angle       4.61211 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.206 
Fit side-chains
REVERT: I   33 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5996 (ttpm)
REVERT: I   49 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6337 (mt-10)
REVERT: I   78 SER cc_start: 0.8472 (t) cc_final: 0.8262 (p)
REVERT: I  124 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6580 (pt0)
REVERT: I  223 ARG cc_start: 0.7562 (ttt180) cc_final: 0.6995 (ttp80)
REVERT: J   13 GLU cc_start: 0.6843 (pt0) cc_final: 0.6221 (pt0)
REVERT: J   25 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7504 (m)
REVERT: J   68 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6452 (mm-30)
REVERT: J   83 HIS cc_start: 0.4558 (OUTLIER) cc_final: 0.3231 (m90)
REVERT: J  153 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7522 (mt)
REVERT: J  171 HIS cc_start: 0.7114 (p-80) cc_final: 0.6814 (p90)
REVERT: J  188 ARG cc_start: 0.6601 (mmm160) cc_final: 0.6234 (mmm-85)
  outliers start: 24
  outliers final: 12
  residues processed: 110
  average time/residue: 0.6037
  time to fit residues: 68.7674
Evaluate side-chains
  110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   33 LYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  124 GLN
Chi-restraints excluded: chain I residue  141 GLU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  137 ASP
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0070
   chunk 59 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.6006

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 247 GLN
I 275 GLN
J 105 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.156259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.131191 restraints weight = 12926.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.12
r_work: 0.3295 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5156  Z= 0.134
  Angle     :  0.548   5.784   6981  Z= 0.279
  Chirality :  0.041   0.134    766
  Planarity :  0.005   0.042    885
  Dihedral  :  7.992  81.443    708
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.49 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 17.10 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.33), residues: 602
  helix:  1.91 (0.28), residues: 337
  sheet:  1.98 (1.10), residues: 14
  loop : -0.58 (0.36), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG I 197 
 TYR   0.016   0.001   TYR I  60 
 PHE   0.015   0.001   PHE I  71 
 TRP   0.013   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5156)
  covalent geometry    : angle       0.54822 ( 6981)
  hydrogen bonds       : bond        0.04714 (  267)
  hydrogen bonds       : angle       4.50622 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.195 
Fit side-chains
REVERT: I   33 LYS cc_start: 0.6360 (OUTLIER) cc_final: 0.6014 (ttpm)
REVERT: I   49 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6383 (mt-10)
REVERT: I   78 SER cc_start: 0.8411 (t) cc_final: 0.8196 (p)
REVERT: I  124 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6540 (pt0)
REVERT: I  223 ARG cc_start: 0.7520 (ttt180) cc_final: 0.7018 (ttp80)
REVERT: I  250 ASP cc_start: 0.7175 (m-30) cc_final: 0.6902 (m-30)
REVERT: J   13 GLU cc_start: 0.6798 (pt0) cc_final: 0.6187 (pt0)
REVERT: J   25 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7427 (m)
REVERT: J   68 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6470 (mm-30)
REVERT: J   83 HIS cc_start: 0.4541 (OUTLIER) cc_final: 0.3265 (m90)
REVERT: J  153 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7465 (mt)
REVERT: J  188 ARG cc_start: 0.6524 (mmm160) cc_final: 0.6139 (mmm-85)
  outliers start: 25
  outliers final: 14
  residues processed: 111
  average time/residue: 0.6584
  time to fit residues: 75.5563
Evaluate side-chains
  112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  275 VAL
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain I residue   12 THR
Chi-restraints excluded: chain I residue   33 LYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  124 GLN
Chi-restraints excluded: chain I residue  141 GLU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  119 LEU
Chi-restraints excluded: chain J residue  137 ASP
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.0970
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 247 GLN
I 275 GLN
J 105 ASN
J 171 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.157337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.131284 restraints weight = 14206.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.34
r_work: 0.3280 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5156  Z= 0.118
  Angle     :  0.524   6.228   6981  Z= 0.268
  Chirality :  0.040   0.134    766
  Planarity :  0.005   0.040    885
  Dihedral  :  7.934  82.688    708
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.16 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 17.83 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.33), residues: 602
  helix:  2.05 (0.28), residues: 337
  sheet:  1.98 (1.12), residues: 14
  loop : -0.52 (0.36), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG I 197 
 TYR   0.015   0.001   TYR I  60 
 PHE   0.014   0.001   PHE I 110 
 TRP   0.012   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5156)
  covalent geometry    : angle       0.52436 ( 6981)
  hydrogen bonds       : bond        0.04371 (  267)
  hydrogen bonds       : angle       4.40200 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.205 
Fit side-chains
REVERT: H  253 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7040 (mp)
REVERT: I    9 ARG cc_start: 0.6875 (tpm170) cc_final: 0.6628 (tpm170)
REVERT: I   33 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5965 (ttpm)
REVERT: I   49 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6258 (mt-10)
REVERT: I  124 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.6516 (pt0)
REVERT: I  223 ARG cc_start: 0.7549 (ttt180) cc_final: 0.6997 (ttp80)
REVERT: I  250 ASP cc_start: 0.7248 (m-30) cc_final: 0.6967 (m-30)
REVERT: J   13 GLU cc_start: 0.6824 (pt0) cc_final: 0.6204 (pt0)
REVERT: J   68 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6626 (mm-30)
REVERT: J   83 HIS cc_start: 0.4590 (OUTLIER) cc_final: 0.3281 (m90)
REVERT: J  153 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7446 (mt)
REVERT: J  188 ARG cc_start: 0.6559 (mmm160) cc_final: 0.6185 (mmm-85)
  outliers start: 23
  outliers final: 11
  residues processed: 105
  average time/residue: 0.6584
  time to fit residues: 71.5276
Evaluate side-chains
  106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  253 ILE
Chi-restraints excluded: chain H residue  275 VAL
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain I residue   33 LYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  124 GLN
Chi-restraints excluded: chain I residue  141 GLU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  119 LEU
Chi-restraints excluded: chain J residue  145 LEU
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    0.3980
   chunk 2 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 247 GLN
I 275 GLN
J 105 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.156927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.131626 restraints weight = 16041.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.51
r_work: 0.3300 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3299
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5156  Z= 0.129
  Angle     :  0.539   6.571   6981  Z= 0.275
  Chirality :  0.041   0.135    766
  Planarity :  0.005   0.044    885
  Dihedral  :  7.978  83.311    708
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.33 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.01 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.33), residues: 602
  helix:  2.03 (0.28), residues: 337
  sheet:  1.89 (1.10), residues: 14
  loop : -0.52 (0.36), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG I 197 
 TYR   0.016   0.001   TYR I  60 
 PHE   0.013   0.001   PHE I  71 
 TRP   0.012   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5156)
  covalent geometry    : angle       0.53882 ( 6981)
  hydrogen bonds       : bond        0.04552 (  267)
  hydrogen bonds       : angle       4.40424 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.204 
Fit side-chains
REVERT: H  253 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7045 (mp)
REVERT: I   33 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5960 (ttpm)
REVERT: I   49 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6427 (mt-10)
REVERT: I  124 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6524 (pt0)
REVERT: I  223 ARG cc_start: 0.7496 (ttt180) cc_final: 0.7006 (ttp80)
REVERT: I  250 ASP cc_start: 0.7195 (m-30) cc_final: 0.6917 (m-30)
REVERT: J   13 GLU cc_start: 0.6804 (pt0) cc_final: 0.6182 (pt0)
REVERT: J   25 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7442 (m)
REVERT: J   68 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6627 (mm-30)
REVERT: J   83 HIS cc_start: 0.4561 (OUTLIER) cc_final: 0.3295 (m90)
REVERT: J  153 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7467 (mt)
  outliers start: 21
  outliers final: 12
  residues processed: 104
  average time/residue: 0.7148
  time to fit residues: 76.7526
Evaluate side-chains
  106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  253 ILE
Chi-restraints excluded: chain H residue  275 VAL
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain I residue   33 LYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  124 GLN
Chi-restraints excluded: chain I residue  141 GLU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  119 LEU
Chi-restraints excluded: chain J residue  137 ASP
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 247 GLN
I 275 GLN
J 105 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.157169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.132154 restraints weight = 12292.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.06
r_work: 0.3314 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3306
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.1159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5156  Z= 0.130
  Angle     :  0.556  10.483   6981  Z= 0.281
  Chirality :  0.041   0.135    766
  Planarity :  0.005   0.045    885
  Dihedral  :  7.988  83.401    708
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.49 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.57 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.33), residues: 602
  helix:  2.03 (0.28), residues: 337
  sheet:  1.85 (1.10), residues: 14
  loop : -0.51 (0.36), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG I 197 
 TYR   0.016   0.001   TYR I  60 
 PHE   0.013   0.001   PHE I  71 
 TRP   0.011   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5156)
  covalent geometry    : angle       0.55650 ( 6981)
  hydrogen bonds       : bond        0.04527 (  267)
  hydrogen bonds       : angle       4.40112 (  750)

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

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

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1204 Ramachandran restraints generated.
    602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.188 
Fit side-chains
REVERT: H  253 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7042 (mp)
REVERT: I   33 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5966 (ttpm)
REVERT: I   49 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6365 (mt-10)
REVERT: I  223 ARG cc_start: 0.7500 (ttt180) cc_final: 0.7020 (ttp80)
REVERT: I  250 ASP cc_start: 0.7189 (m-30) cc_final: 0.6916 (m-30)
REVERT: J   13 GLU cc_start: 0.6792 (pt0) cc_final: 0.6166 (pt0)
REVERT: J   25 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7428 (m)
REVERT: J   68 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6631 (mm-30)
REVERT: J   83 HIS cc_start: 0.4547 (OUTLIER) cc_final: 0.3301 (m90)
REVERT: J  105 ASN cc_start: 0.7380 (m-40) cc_final: 0.7122 (t0)
REVERT: J  153 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7449 (mt)
  outliers start: 19
  outliers final: 12
  residues processed: 102
  average time/residue: 0.6980
  time to fit residues: 73.6468
Evaluate side-chains
  104 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  245 LEU
Chi-restraints excluded: chain H residue  253 ILE
Chi-restraints excluded: chain H residue  275 VAL
Chi-restraints excluded: chain H residue  307 GLN
Chi-restraints excluded: chain I residue   33 LYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  141 GLU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  119 LEU
Chi-restraints excluded: chain J residue  137 ASP
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  257 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
I 155 ASN
I 247 GLN
I 275 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.156068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.130657 restraints weight = 21590.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 3.54
r_work: 0.3235 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5156  Z= 0.161
  Angle     :  0.596   8.160   6981  Z= 0.301
  Chirality :  0.043   0.135    766
  Planarity :  0.005   0.046    885
  Dihedral  :  8.129  83.137    708
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.33 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.83 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.33), residues: 602
  helix:  1.88 (0.28), residues: 336
  sheet:  1.70 (1.10), residues: 14
  loop : -0.57 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG I 197 
 TYR   0.017   0.002   TYR I  60 
 PHE   0.016   0.002   PHE I  71 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 5156)
  covalent geometry    : angle       0.59577 ( 6981)
  hydrogen bonds       : bond        0.05042 (  267)
  hydrogen bonds       : angle       4.52903 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2048.51 seconds
wall clock time: 35 minutes 42.11 seconds (2142.11 seconds total)