Starting phenix.real_space_refine
on Fri Aug 22 14:03:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yrj_39543/08_2025/8yrj_39543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yrj_39543/08_2025/8yrj_39543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yrj_39543/08_2025/8yrj_39543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yrj_39543/08_2025/8yrj_39543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yrj_39543/08_2025/8yrj_39543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yrj_39543/08_2025/8yrj_39543.cif"
  }
  resolution = 3.87
  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=   0.006
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      21      5.16       5
     C    2442      2.51       5
     N     597      2.21       5
     O     688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3748
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1743
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 208}
    Chain: "G"
      Number of atoms: 297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 297
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "H"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 341
          Classifications: {'peptide': 43}
          Link IDs: {'PTRANS': 1, 'TRANS': 41}
    Chain: "B"
      Number of atoms: 1247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1247
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 1, 'TRANS': 158}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 0.98, per 1000 atoms: 0.26
  Number of scatterers: 3748
  At special positions: 0
  Unit cell: (57.27, 74.7, 118.69, 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      21     16.00
     O     688      8.00
     N     597      7.00
     C    2442      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  25 " - pdb=" SG  CYS H  25 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 154 " - pdb=" SG  CYS B 163 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A 301 " - " ASN A  73 "
      " NAG A 302 " - " ASN A 167 "
      " NAG A 303 " - " ASN A 152 "
      " NAG C   1 " - " ASN A  66 "
      " NAG D   1 " - " ASN A 106 "
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 88.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  858

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 6 sheets defined
      56.2% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 205 through 236
    Processing helix  chain 'G' and resid 23 through 58
    Processing helix  chain 'H' and resid 21 through 62
      removed outlier: 3.945A  pdb=" N   CYS H  25 " --> pdb=" O   GLU H  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 75
      removed outlier: 5.267A  pdb=" N   LYS B  47 " --> pdb=" O   ARG B  43 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   LYS B  48 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU B  49 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   GLU B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 111
    Processing helix  chain 'B' and resid 117 through 154
      removed outlier: 4.115A  pdb=" N   GLY B 121 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE B 131 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 199
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 3.638A  pdb=" N   THR A 108 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 116
    Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121
      removed outlier: 4.289A  pdb=" N   TYR A 177 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   LYS A 141 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL A 142 " --> pdb=" O   TYR A 153 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   TYR A 153 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   TYR A 144 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127
      removed outlier: 3.766A  pdb=" N   GLY A 125 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE A 127 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   ARG A 162 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    732 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: 0.47

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1124
        1.35 -     1.46: 980
        1.46 -     1.58: 1692
        1.58 -     1.70: 0
        1.70 -     1.82: 27
  Bond restraints: 3823
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.81e+00
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.551 -0.032 2.00e-02 2.50e+03 2.58e+00
  bond pdb=" C1  NAG A 302 "
       pdb=" O5  NAG A 302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.55e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.20e+00
  ... (remaining 3818 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 5021
        1.24 -     2.47: 117
        2.47 -     3.71: 24
        3.71 -     4.95: 12
        4.95 -     6.18: 9
  Bond angle restraints: 5183
  Sorted by residual:
  angle pdb=" C   CYS A 198 "
        pdb=" N   LYS A 199 "
        pdb=" CA  LYS A 199 "
      ideal   model   delta    sigma   weight residual
     121.54  126.03   -4.49 1.91e+00 2.74e-01 5.53e+00
  angle pdb=" C   GLN B  40 "
        pdb=" N   THR B  41 "
        pdb=" CA  THR B  41 "
      ideal   model   delta    sigma   weight residual
     121.54  125.78   -4.24 1.91e+00 2.74e-01 4.93e+00
  angle pdb=" N   GLU H  21 "
        pdb=" CA  GLU H  21 "
        pdb=" C   GLU H  21 "
      ideal   model   delta    sigma   weight residual
     109.81  114.50   -4.69 2.21e+00 2.05e-01 4.50e+00
  angle pdb=" C3  BMA C   3 "
        pdb=" C2  BMA C   3 "
        pdb=" O2  BMA C   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.77    6.18 3.00e+00 1.11e-01 4.25e+00
  angle pdb=" C3  BMA D   3 "
        pdb=" C2  BMA D   3 "
        pdb=" O2  BMA D   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.79    6.16 3.00e+00 1.11e-01 4.22e+00
  ... (remaining 5178 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.39: 2161
       23.39 -    46.78: 161
       46.78 -    70.17: 25
       70.17 -    93.56: 17
       93.56 -   116.95: 11
  Dihedral angle restraints: 2375
    sinusoidal: 1042
      harmonic: 1333
  Sorted by residual:
  dihedral pdb=" CB  CYS G  25 "
           pdb=" SG  CYS G  25 "
           pdb=" SG  CYS H  25 "
           pdb=" CB  CYS H  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.20  -81.20     1      1.00e+01 1.00e-02 8.13e+01
  dihedral pdb=" C1  NAG C   2 "
           pdb=" C5  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   52.84 -116.95     1      3.00e+01 1.11e-03 1.55e+01
  dihedral pdb=" C1  NAG C   2 "
           pdb=" C5  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C6  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -72.39 -116.45     1      3.00e+01 1.11e-03 1.54e+01
  ... (remaining 2372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 540
       0.054 -    0.108: 82
       0.108 -    0.161: 14
       0.161 -    0.215: 0
       0.215 -    0.269: 2
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" C2  BMA C   3 "
            pdb=" C1  BMA C   3 "
            pdb=" C3  BMA C   3 "
            pdb=" O2  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.62   -0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 635 not shown)

  Planarity restraints: 620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 207 "   -0.022 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A 208 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 208 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 208 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 157 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO A 158 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 158 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 158 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  56 "   -0.005 2.00e-02 2.50e+03   9.38e-03 8.79e-01
        pdb=" C   GLN A  56 "    0.016 2.00e-02 2.50e+03
        pdb=" O   GLN A  56 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   MET A  57 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 617 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 654
        2.77 -     3.30: 3630
        3.30 -     3.84: 6313
        3.84 -     4.37: 6566
        4.37 -     4.90: 11859
  Nonbonded interactions: 29022
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 168 "
            pdb=" OH  TYR A 172 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG1 THR B  41 "
            pdb=" N   TRP B  42 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OG  SER A 154 "
            pdb=" O   SER A 157 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   LEU A 221 "
            pdb=" OG1 THR A 225 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" O   ASP A  86 "
            pdb=" OH  TYR A  90 "
     model   vdw
     2.375 3.040
  ... (remaining 29017 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'G'
  selection = (chain 'H' and resid 22 through 58)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.680
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.830
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   3836  Z= 0.170
  Angle     :  0.569   6.185   5218  Z= 0.262
  Chirality :  0.042   0.269    638
  Planarity :  0.003   0.033    615
  Dihedral  : 19.292 116.955   1505
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  3.59 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.47 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.42), residues: 446
  helix:  3.31 (0.31), residues: 232
  sheet:  0.83 (0.61), residues: 71
  loop : -1.08 (0.58), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 162 
 TYR   0.007   0.001   TYR A  50 
 PHE   0.006   0.001   PHE B 168 
 TRP   0.006   0.001   TRP B  42 
 HIS   0.001   0.000   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3823)
  covalent geometry    : angle       0.54169 ( 5183)
  SS BOND              : bond        0.00310 (    4)
  SS BOND              : angle       0.90827 (    8)
  hydrogen bonds       : bond        0.10320 (  251)
  hydrogen bonds       : angle       4.01228 (  732)
  link_BETA1-4         : bond        0.00844 (    4)
  link_BETA1-4         : angle       1.95186 (   12)
  link_NAG-ASN         : bond        0.00353 (    5)
  link_NAG-ASN         : angle       2.80331 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8195 (tttt) cc_final: 0.7871 (ttpt)
REVERT: A   93 GLN cc_start: 0.7156 (tt0) cc_final: 0.6788 (tm-30)
REVERT: A  128 ASP cc_start: 0.8230 (m-30) cc_final: 0.7994 (m-30)
REVERT: A  144 TYR cc_start: 0.7097 (m-80) cc_final: 0.6446 (m-80)
REVERT: A  203 LEU cc_start: 0.9533 (mt) cc_final: 0.9282 (mt)
REVERT: H   33 PHE cc_start: 0.8736 (t80) cc_final: 0.8306 (t80)
REVERT: B  109 ILE cc_start: 0.9025 (mm) cc_final: 0.8652 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0638
  time to fit residues: 14.9003
Evaluate side-chains
  125 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 173 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.180700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.155313 restraints weight = 7851.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.159305 restraints weight = 4831.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.162032 restraints weight = 3380.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.163899 restraints weight = 2597.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.165154 restraints weight = 2138.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3836  Z= 0.204
  Angle     :  0.912  17.821   5218  Z= 0.417
  Chirality :  0.050   0.289    638
  Planarity :  0.004   0.035    615
  Dihedral  : 15.358  90.621    677
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.48 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 21.45 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.40), residues: 446
  helix:  3.03 (0.31), residues: 227
  sheet: -0.10 (0.62), residues: 69
  loop : -1.03 (0.52), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 194 
 TYR   0.041   0.002   TYR H  26 
 PHE   0.031   0.002   PHE B  45 
 TRP   0.014   0.002   TRP A 137 
 HIS   0.008   0.002   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 3823)
  covalent geometry    : angle       0.79171 ( 5183)
  SS BOND              : bond        0.00817 (    4)
  SS BOND              : angle       3.27492 (    8)
  hydrogen bonds       : bond        0.04282 (  251)
  hydrogen bonds       : angle       3.90017 (  732)
  link_BETA1-4         : bond        0.01095 (    4)
  link_BETA1-4         : angle       2.98494 (   12)
  link_NAG-ASN         : bond        0.01202 (    5)
  link_NAG-ASN         : angle       7.73227 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8207 (p90) cc_final: 0.7805 (p90)
REVERT: A  137 TRP cc_start: 0.7035 (m-10) cc_final: 0.6626 (m-10)
REVERT: A  144 TYR cc_start: 0.7090 (m-80) cc_final: 0.6715 (m-10)
REVERT: A  202 TRP cc_start: 0.9035 (p-90) cc_final: 0.8654 (p-90)
REVERT: A  222 LEU cc_start: 0.8808 (tt) cc_final: 0.8397 (tp)
REVERT: H   33 PHE cc_start: 0.8840 (t80) cc_final: 0.8400 (t80)
REVERT: B   79 ASP cc_start: 0.8374 (m-30) cc_final: 0.8144 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 140
  average time/residue: 0.0655
  time to fit residues: 11.3921
Evaluate side-chains
  131 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.176457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.150045 restraints weight = 7624.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.154085 restraints weight = 4568.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.156859 restraints weight = 3196.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.158766 restraints weight = 2467.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.160115 restraints weight = 2045.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.4371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3836  Z= 0.185
  Angle     :  0.870  14.520   5218  Z= 0.400
  Chirality :  0.049   0.227    638
  Planarity :  0.003   0.032    615
  Dihedral  : 11.538  71.512    677
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.48 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 22.44 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.39), residues: 446
  helix:  2.26 (0.32), residues: 236
  sheet:  0.07 (0.61), residues: 69
  loop : -1.18 (0.51), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 194 
 TYR   0.027   0.002   TYR H  26 
 PHE   0.012   0.002   PHE B  52 
 TRP   0.010   0.002   TRP A 134 
 HIS   0.007   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3823)
  covalent geometry    : angle       0.78491 ( 5183)
  SS BOND              : bond        0.00944 (    4)
  SS BOND              : angle       1.77808 (    8)
  hydrogen bonds       : bond        0.04359 (  251)
  hydrogen bonds       : angle       3.98966 (  732)
  link_BETA1-4         : bond        0.00847 (    4)
  link_BETA1-4         : angle       3.33777 (   12)
  link_NAG-ASN         : bond        0.01059 (    5)
  link_NAG-ASN         : angle       6.31127 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8484 (p90) cc_final: 0.8091 (p90)
REVERT: A  144 TYR cc_start: 0.7123 (m-80) cc_final: 0.6716 (m-10)
REVERT: A  204 GLN cc_start: 0.8692 (tp40) cc_final: 0.8146 (tp40)
REVERT: B   79 ASP cc_start: 0.8502 (m-30) cc_final: 0.8250 (p0)
  outliers start: 16
  outliers final: 13
  residues processed: 144
  average time/residue: 0.0527
  time to fit residues: 9.6527
Evaluate side-chains
  134 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.168988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.142539 restraints weight = 7563.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.146504 restraints weight = 4376.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.149259 restraints weight = 3015.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.151225 restraints weight = 2317.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.152431 restraints weight = 1902.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.5612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3836  Z= 0.254
  Angle     :  0.942  13.404   5218  Z= 0.436
  Chirality :  0.053   0.263    638
  Planarity :  0.004   0.030    615
  Dihedral  :  8.320  58.198    677
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.93 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  7.48 %
    Allowed  : 23.94 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.39), residues: 446
  helix:  1.81 (0.31), residues: 228
  sheet: -0.37 (0.58), residues: 67
  loop : -1.30 (0.52), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 194 
 TYR   0.026   0.003   TYR A 200 
 PHE   0.034   0.003   PHE A  40 
 TRP   0.018   0.002   TRP A 137 
 HIS   0.005   0.002   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 3823)
  covalent geometry    : angle       0.86563 ( 5183)
  SS BOND              : bond        0.01701 (    4)
  SS BOND              : angle       1.29755 (    8)
  hydrogen bonds       : bond        0.04940 (  251)
  hydrogen bonds       : angle       4.34559 (  732)
  link_BETA1-4         : bond        0.00580 (    4)
  link_BETA1-4         : angle       3.59765 (   12)
  link_NAG-ASN         : bond        0.00845 (    5)
  link_NAG-ASN         : angle       6.21351 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8071 (m-10) cc_final: 0.7499 (m-10)
REVERT: A  127 PHE cc_start: 0.8615 (p90) cc_final: 0.8302 (p90)
REVERT: A  144 TYR cc_start: 0.7230 (m-80) cc_final: 0.6757 (m-10)
REVERT: A  204 GLN cc_start: 0.8746 (tp40) cc_final: 0.8227 (tp40)
REVERT: B   52 PHE cc_start: 0.8926 (t80) cc_final: 0.8721 (t80)
REVERT: B  148 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6161 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 158
  average time/residue: 0.0500
  time to fit residues: 10.1144
Evaluate side-chains
  148 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain G residue   32 LEU
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.170326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.144007 restraints weight = 7660.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.147992 restraints weight = 4508.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.150716 restraints weight = 3129.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.152474 restraints weight = 2411.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.153873 restraints weight = 2011.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.6025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3836  Z= 0.165
  Angle     :  0.830  12.949   5218  Z= 0.390
  Chirality :  0.049   0.304    638
  Planarity :  0.003   0.032    615
  Dihedral  :  7.556  58.466    677
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.26 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 27.93 %
    Favored  : 66.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.39), residues: 446
  helix:  1.98 (0.32), residues: 225
  sheet: -0.02 (0.65), residues: 60
  loop : -1.12 (0.50), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.023   0.002   TYR B 193 
 PHE   0.027   0.002   PHE B 168 
 TRP   0.015   0.002   TRP B  95 
 HIS   0.002   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3823)
  covalent geometry    : angle       0.75284 ( 5183)
  SS BOND              : bond        0.00899 (    4)
  SS BOND              : angle       1.05931 (    8)
  hydrogen bonds       : bond        0.04623 (  251)
  hydrogen bonds       : angle       4.10606 (  732)
  link_BETA1-4         : bond        0.00871 (    4)
  link_BETA1-4         : angle       3.58722 (   12)
  link_NAG-ASN         : bond        0.01076 (    5)
  link_NAG-ASN         : angle       5.75262 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8105 (m-10) cc_final: 0.7558 (m-10)
REVERT: A  135 LYS cc_start: 0.8292 (ttpt) cc_final: 0.8086 (ttpt)
REVERT: A  144 TYR cc_start: 0.7236 (m-80) cc_final: 0.6774 (m-10)
REVERT: A  204 GLN cc_start: 0.8680 (tp40) cc_final: 0.8193 (tp40)
REVERT: B  150 TYR cc_start: 0.9009 (t80) cc_final: 0.8773 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 148
  average time/residue: 0.0618
  time to fit residues: 11.5374
Evaluate side-chains
  148 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  161 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0970
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.168708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.142015 restraints weight = 7720.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.145710 restraints weight = 4725.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.148307 restraints weight = 3368.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.150110 restraints weight = 2634.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.151448 restraints weight = 2213.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.6262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   3836  Z= 0.166
  Angle     :  0.834  12.302   5218  Z= 0.393
  Chirality :  0.049   0.302    638
  Planarity :  0.003   0.031    615
  Dihedral  :  7.098  58.750    677
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.71 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 29.68 %
    Favored  : 65.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.40), residues: 446
  helix:  2.25 (0.32), residues: 222
  sheet: -0.26 (0.65), residues: 60
  loop : -1.23 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 194 
 TYR   0.020   0.002   TYR B  92 
 PHE   0.034   0.002   PHE A 127 
 TRP   0.014   0.001   TRP B  95 
 HIS   0.002   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3823)
  covalent geometry    : angle       0.76251 ( 5183)
  SS BOND              : bond        0.00694 (    4)
  SS BOND              : angle       1.06727 (    8)
  hydrogen bonds       : bond        0.04564 (  251)
  hydrogen bonds       : angle       4.06907 (  732)
  link_BETA1-4         : bond        0.00853 (    4)
  link_BETA1-4         : angle       3.45967 (   12)
  link_NAG-ASN         : bond        0.01077 (    5)
  link_NAG-ASN         : angle       5.54965 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8068 (m-10) cc_final: 0.7606 (m-10)
REVERT: A  129 ILE cc_start: 0.8778 (mp) cc_final: 0.8397 (mp)
REVERT: A  144 TYR cc_start: 0.7131 (m-80) cc_final: 0.6666 (m-10)
REVERT: A  204 GLN cc_start: 0.8571 (tp40) cc_final: 0.8080 (tp40)
REVERT: B   49 GLU cc_start: 0.6517 (mp0) cc_final: 0.5973 (pt0)
REVERT: B  148 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.5963 (t80)
REVERT: B  150 TYR cc_start: 0.9077 (t80) cc_final: 0.8804 (t80)
  outliers start: 20
  outliers final: 14
  residues processed: 147
  average time/residue: 0.0604
  time to fit residues: 11.4242
Evaluate side-chains
  147 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   29 ASP
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.168465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.141595 restraints weight = 7852.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.145309 restraints weight = 4866.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.147728 restraints weight = 3457.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.149650 restraints weight = 2734.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.150590 restraints weight = 2283.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.6423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3836  Z= 0.169
  Angle     :  0.834  11.713   5218  Z= 0.397
  Chirality :  0.049   0.320    638
  Planarity :  0.003   0.032    615
  Dihedral  :  6.890  56.600    677
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.48 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 31.42 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.39), residues: 446
  helix:  2.13 (0.31), residues: 222
  sheet: -0.52 (0.64), residues: 60
  loop : -1.24 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 194 
 TYR   0.020   0.002   TYR B  92 
 PHE   0.041   0.002   PHE A 127 
 TRP   0.015   0.002   TRP B  95 
 HIS   0.005   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3823)
  covalent geometry    : angle       0.76691 ( 5183)
  SS BOND              : bond        0.00641 (    4)
  SS BOND              : angle       0.93723 (    8)
  hydrogen bonds       : bond        0.04517 (  251)
  hydrogen bonds       : angle       4.11524 (  732)
  link_BETA1-4         : bond        0.00698 (    4)
  link_BETA1-4         : angle       3.35081 (   12)
  link_NAG-ASN         : bond        0.00989 (    5)
  link_NAG-ASN         : angle       5.40972 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8153 (m-10) cc_final: 0.7569 (m-10)
REVERT: B  148 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.5786 (t80)
REVERT: B  150 TYR cc_start: 0.9061 (t80) cc_final: 0.8714 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 145
  average time/residue: 0.0574
  time to fit residues: 10.8204
Evaluate side-chains
  145 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain G residue   29 ASP
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    0.0570
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.169416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.142376 restraints weight = 7782.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.145929 restraints weight = 4913.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.148404 restraints weight = 3567.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.150035 restraints weight = 2835.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.151305 restraints weight = 2416.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.6613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3836  Z= 0.161
  Angle     :  0.836  11.188   5218  Z= 0.394
  Chirality :  0.048   0.327    638
  Planarity :  0.003   0.032    615
  Dihedral  :  6.764  55.626    677
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.26 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 31.17 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.39), residues: 446
  helix:  2.08 (0.31), residues: 225
  sheet: -0.25 (0.66), residues: 60
  loop : -1.33 (0.51), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 194 
 TYR   0.019   0.002   TYR B  92 
 PHE   0.038   0.002   PHE A 127 
 TRP   0.015   0.002   TRP B  95 
 HIS   0.006   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3823)
  covalent geometry    : angle       0.77394 ( 5183)
  SS BOND              : bond        0.00598 (    4)
  SS BOND              : angle       1.13773 (    8)
  hydrogen bonds       : bond        0.04442 (  251)
  hydrogen bonds       : angle       4.15367 (  732)
  link_BETA1-4         : bond        0.00780 (    4)
  link_BETA1-4         : angle       3.25014 (   12)
  link_NAG-ASN         : bond        0.01029 (    5)
  link_NAG-ASN         : angle       5.19365 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8156 (m-10) cc_final: 0.7570 (m-10)
REVERT: A  144 TYR cc_start: 0.6639 (m-10) cc_final: 0.6165 (m-10)
REVERT: B   58 ILE cc_start: 0.8390 (mm) cc_final: 0.8161 (mp)
REVERT: B  148 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.5849 (t80)
REVERT: B  150 TYR cc_start: 0.9081 (t80) cc_final: 0.8682 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 154
  average time/residue: 0.0566
  time to fit residues: 11.1654
Evaluate side-chains
  149 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   29 ASP
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 18 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.167551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.141188 restraints weight = 7712.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.144675 restraints weight = 4778.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.147086 restraints weight = 3420.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.148906 restraints weight = 2707.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.150028 restraints weight = 2278.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.6894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097   3836  Z= 0.193
  Angle     :  0.903  12.140   5218  Z= 0.426
  Chirality :  0.050   0.345    638
  Planarity :  0.003   0.032    615
  Dihedral  :  6.839  54.578    677
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  5.16 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 31.92 %
    Favored  : 63.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.39), residues: 446
  helix:  1.90 (0.31), residues: 225
  sheet: -0.17 (0.63), residues: 63
  loop : -1.39 (0.51), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 194 
 TYR   0.019   0.002   TYR B  92 
 PHE   0.035   0.002   PHE A 127 
 TRP   0.016   0.002   TRP A 202 
 HIS   0.005   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 3823)
  covalent geometry    : angle       0.84681 ( 5183)
  SS BOND              : bond        0.00634 (    4)
  SS BOND              : angle       1.48938 (    8)
  hydrogen bonds       : bond        0.04521 (  251)
  hydrogen bonds       : angle       4.40341 (  732)
  link_BETA1-4         : bond        0.00676 (    4)
  link_BETA1-4         : angle       3.15924 (   12)
  link_NAG-ASN         : bond        0.00901 (    5)
  link_NAG-ASN         : angle       5.13905 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8218 (m-10) cc_final: 0.7595 (m-10)
REVERT: B   88 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.8107 (m-80)
  outliers start: 20
  outliers final: 17
  residues processed: 147
  average time/residue: 0.0557
  time to fit residues: 10.4929
Evaluate side-chains
  150 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain G residue   29 ASP
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0050
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.168562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.140423 restraints weight = 8166.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.144354 restraints weight = 4931.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.147108 restraints weight = 3490.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.148870 restraints weight = 2719.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.150346 restraints weight = 2295.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.7019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089   3836  Z= 0.176
  Angle     :  0.884  11.278   5218  Z= 0.417
  Chirality :  0.049   0.370    638
  Planarity :  0.003   0.032    615
  Dihedral  :  6.770  54.536    677
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  5.38 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 32.67 %
    Favored  : 62.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.39), residues: 446
  helix:  1.96 (0.31), residues: 225
  sheet: -0.05 (0.63), residues: 63
  loop : -1.43 (0.51), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 194 
 TYR   0.019   0.002   TYR B  92 
 PHE   0.036   0.002   PHE A 127 
 TRP   0.017   0.002   TRP A 202 
 HIS   0.006   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3823)
  covalent geometry    : angle       0.83083 ( 5183)
  SS BOND              : bond        0.00605 (    4)
  SS BOND              : angle       1.49494 (    8)
  hydrogen bonds       : bond        0.04545 (  251)
  hydrogen bonds       : angle       4.34203 (  732)
  link_BETA1-4         : bond        0.00790 (    4)
  link_BETA1-4         : angle       3.06489 (   12)
  link_NAG-ASN         : bond        0.00933 (    5)
  link_NAG-ASN         : angle       4.98578 (   15)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8291 (m-10) cc_final: 0.7558 (m-10)
REVERT: A  168 ASP cc_start: 0.7831 (m-30) cc_final: 0.7603 (t0)
REVERT: H   39 LEU cc_start: 0.8310 (tp) cc_final: 0.8017 (tp)
REVERT: B  155 LYS cc_start: 0.7933 (mptt) cc_final: 0.7181 (pttp)
  outliers start: 18
  outliers final: 16
  residues processed: 146
  average time/residue: 0.0601
  time to fit residues: 11.0784
Evaluate side-chains
  149 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain G residue   29 ASP
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 10 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.167352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.140110 restraints weight = 7901.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.143673 restraints weight = 5040.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.146153 restraints weight = 3694.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.147811 restraints weight = 2948.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.149040 restraints weight = 2525.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.7220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   3836  Z= 0.178
  Angle     :  0.877  11.381   5218  Z= 0.417
  Chirality :  0.048   0.340    638
  Planarity :  0.003   0.031    615
  Dihedral  :  6.790  53.631    677
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  :  4.71 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 34.16 %
    Favored  : 61.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.39), residues: 446
  helix:  1.98 (0.31), residues: 226
  sheet: -0.19 (0.59), residues: 70
  loop : -1.46 (0.52), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 194 
 TYR   0.018   0.002   TYR B  92 
 PHE   0.033   0.002   PHE A 127 
 TRP   0.017   0.002   TRP B  95 
 HIS   0.006   0.001   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 3823)
  covalent geometry    : angle       0.82587 ( 5183)
  SS BOND              : bond        0.00581 (    4)
  SS BOND              : angle       1.55382 (    8)
  hydrogen bonds       : bond        0.04424 (  251)
  hydrogen bonds       : angle       4.35807 (  732)
  link_BETA1-4         : bond        0.00694 (    4)
  link_BETA1-4         : angle       3.00092 (   12)
  link_NAG-ASN         : bond        0.00872 (    5)
  link_NAG-ASN         : angle       4.85740 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 817.91 seconds
wall clock time: 14 minutes 48.73 seconds (888.73 seconds total)