Starting phenix.real_space_refine
on Tue Feb  3 17:01:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u92_63956/02_2026/9u92_63956.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u92_63956/02_2026/9u92_63956.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u92_63956/02_2026/9u92_63956.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u92_63956/02_2026/9u92_63956.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u92_63956/02_2026/9u92_63956.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u92_63956/02_2026/9u92_63956.cif"
  }
  resolution = 2.68
  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=   0.075
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      28      5.16       5
     C    3425      2.51       5
     N     921      2.21       5
     O     998      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5372
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1824
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 216}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2159
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 7, 'TRANS': 254}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 311
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "D"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1051
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 2, 'TRANS': 125}
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Time building chain proxies: 0.94, per 1000 atoms: 0.17
  Number of scatterers: 5372
  At special positions: 0
  Unit cell: (75.44, 82.8, 120.52, 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      28     16.00
     O     998      8.00
     N     921      7.00
     C    3425      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 182.8 milliseconds
  

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1236

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 2 sheets defined
      42.2% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 136 through 166
      removed outlier: 3.644A  pdb=" N   GLN A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LYS A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
      removed outlier: 3.533A  pdb=" N   LEU A 191 " --> pdb=" O   ASN A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 237
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 257 through 268
    Processing helix  chain 'A' and resid 336 through 346
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 3.717A  pdb=" N   LEU A 361 " --> pdb=" O   ARG A 358 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 105
    Processing helix  chain 'B' and resid 106 through 110
    Processing helix  chain 'B' and resid 131 through 135
    Processing helix  chain 'B' and resid 136 through 141
      removed outlier: 4.001A  pdb=" N   GLY B 141 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 172
      removed outlier: 3.944A  pdb=" N   SER B 170 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 203
    Processing helix  chain 'B' and resid 218 through 227
    Processing helix  chain 'B' and resid 320 through 334
    Processing helix  chain 'B' and resid 342 through 346
    Processing helix  chain 'B' and resid 402 through 414
    Processing helix  chain 'C' and resid 152 through 157
      removed outlier: 3.755A  pdb=" N   ILE C 156 " --> pdb=" O   THR C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 185
    Processing helix  chain 'D' and resid 13 through 26
    Processing helix  chain 'D' and resid 51 through 65
    Processing helix  chain 'D' and resid 69 through 78
      removed outlier: 4.041A  pdb=" N   ILE D  73 " --> pdb=" O   ASN D  69 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   PHE D  78 " --> pdb=" O   ASN D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 96
    Processing helix  chain 'D' and resid 100 through 104
    Processing helix  chain 'D' and resid 109 through 127
      removed outlier: 4.495A  pdb=" N   GLU D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   GLU D 115 " --> pdb=" O   GLU D 111 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE D 116 " --> pdb=" O   GLU D 112 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 180
      removed outlier: 6.750A  pdb=" N   TYR A 351 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ILE A 368 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLU A 353 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   VAL A 205 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   ILE A 206 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   TRP A 252 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   MET A 208 " --> pdb=" O   TRP A 252 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER A 301 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL A 306 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   LEU A 272 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   ILE A 324 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   THR A 277 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   SER A 326 " --> pdb=" O   THR A 277 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   VAL A 279 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 129
      removed outlier: 3.758A  pdb=" N   TRP B 187 " --> pdb=" O   ILE B 149 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR B 361 " --> pdb=" O   SER B 188 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ARG B 366 " --> pdb=" O   TYR B 207 " (cutoff:3.500A)
      removed outlier: 5.643A  pdb=" N   TYR B 207 " --> pdb=" O   ARG B 366 " (cutoff:3.500A)

    216 hydrogen bonds defined for protein.
    594 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: 0.64

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1748
        1.34 -     1.46: 1169
        1.46 -     1.58: 2501
        1.58 -     1.70: 0
        1.70 -     1.82: 50
  Bond restraints: 5468
  Sorted by residual:
  bond pdb=" CB  GLN A 144 "
       pdb=" CG  GLN A 144 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 3.00e-02 1.11e+03 2.43e+00
  bond pdb=" N   ASN A 348 "
       pdb=" CA  ASN A 348 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.018 1.29e-02 6.01e+03 1.95e+00
  bond pdb=" CB  ILE A 146 "
       pdb=" CG2 ILE A 146 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.71e+00
  bond pdb=" CB  ILE A 319 "
       pdb=" CG1 ILE A 319 "
    ideal  model  delta    sigma   weight residual
    1.530  1.551 -0.021 2.00e-02 2.50e+03 1.08e+00
  bond pdb=" CA  ASN B 210 "
       pdb=" CB  ASN B 210 "
    ideal  model  delta    sigma   weight residual
    1.535  1.555 -0.021 2.02e-02 2.45e+03 1.04e+00
  ... (remaining 5463 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 7296
        3.21 -     6.42: 42
        6.42 -     9.63: 6
        9.63 -    12.84: 0
       12.84 -    16.05: 1
  Bond angle restraints: 7345
  Sorted by residual:
  angle pdb=" CA  LEU C 170 "
        pdb=" CB  LEU C 170 "
        pdb=" CG  LEU C 170 "
      ideal   model   delta    sigma   weight residual
     116.30  132.35  -16.05 3.50e+00 8.16e-02 2.10e+01
  angle pdb=" C   ALA A 320 "
        pdb=" CA  ALA A 320 "
        pdb=" CB  ALA A 320 "
      ideal   model   delta    sigma   weight residual
     116.34  110.03    6.31 1.40e+00 5.10e-01 2.03e+01
  angle pdb=" CA  GLN A 144 "
        pdb=" CB  GLN A 144 "
        pdb=" CG  GLN A 144 "
      ideal   model   delta    sigma   weight residual
     114.10  121.63   -7.53 2.00e+00 2.50e-01 1.42e+01
  angle pdb=" N   ILE A 146 "
        pdb=" CA  ILE A 146 "
        pdb=" C   ILE A 146 "
      ideal   model   delta    sigma   weight residual
     113.07  108.22    4.85 1.36e+00 5.41e-01 1.27e+01
  angle pdb=" CB  GLN A 144 "
        pdb=" CG  GLN A 144 "
        pdb=" CD  GLN A 144 "
      ideal   model   delta    sigma   weight residual
     112.60  118.29   -5.69 1.70e+00 3.46e-01 1.12e+01
  ... (remaining 7340 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2743
       17.95 -    35.90: 449
       35.90 -    53.84: 130
       53.84 -    71.79: 33
       71.79 -    89.74: 12
  Dihedral angle restraints: 3367
    sinusoidal: 1463
      harmonic: 1904
  Sorted by residual:
  dihedral pdb=" CA  MET B 402 "
           pdb=" C   MET B 402 "
           pdb=" N   LYS B 403 "
           pdb=" CA  LYS B 403 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ASP D  76 "
           pdb=" CB  ASP D  76 "
           pdb=" CG  ASP D  76 "
           pdb=" OD1 ASP D  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.77   59.77     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CA  ILE B 213 "
           pdb=" C   ILE B 213 "
           pdb=" N   MET B 214 "
           pdb=" CA  MET B 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.36   16.64     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 3364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 780
       0.111 -    0.223: 16
       0.223 -    0.334: 0
       0.334 -    0.445: 0
       0.445 -    0.557: 1
  Chirality restraints: 797
  Sorted by residual:
  chirality pdb=" CG  LEU C 170 "
            pdb=" CB  LEU C 170 "
            pdb=" CD1 LEU C 170 "
            pdb=" CD2 LEU C 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.03   -0.56 2.00e-01 2.50e+01 7.75e+00
  chirality pdb=" CB  ILE B 208 "
            pdb=" CA  ILE B 208 "
            pdb=" CG1 ILE B 208 "
            pdb=" CG2 ILE B 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.14e-01
  chirality pdb=" CA  ILE B 213 "
            pdb=" N   ILE B 213 "
            pdb=" C   ILE B 213 "
            pdb=" CB  ILE B 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.66e-01
  ... (remaining 794 not shown)

  Planarity restraints: 936
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 352 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.62e+00
        pdb=" N   PRO B 353 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 353 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 353 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 154 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   LYS A 154 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LYS A 154 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLN A 155 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 157 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.87e+00
        pdb=" C   PHE A 157 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   PHE A 157 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 158 "    0.010 2.00e-02 2.50e+03
  ... (remaining 933 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 926
        2.77 -     3.30: 4995
        3.30 -     3.83: 9207
        3.83 -     4.37: 11130
        4.37 -     4.90: 18461
  Nonbonded interactions: 44719
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" NZ  LYS B 190 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   CYS A 346 "
            pdb=" OH  TYR A 351 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   GLN B 408 "
            pdb=" OG1 THR B 412 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" NE2 GLN A 155 "
            pdb=" O   LYS D 131 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" OH  TYR D  41 "
            pdb=" NZ  LYS D  46 "
     model   vdw
     2.353 3.120
  ... (remaining 44714 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
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      :  0.004   0.047   5468  Z= 0.163
  Angle     :  0.697  16.047   7345  Z= 0.363
  Chirality :  0.048   0.557    797
  Planarity :  0.004   0.048    936
  Dihedral  : 19.819  89.739   2131
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 33.84 %
    Favored  : 62.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.32), residues: 639
  helix:  0.09 (0.32), residues: 232
  sheet: -0.86 (0.51), residues: 91
  loop : -0.79 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 259 
 TYR   0.014   0.001   TYR A 258 
 PHE   0.014   0.001   PHE B 211 
 TRP   0.007   0.001   TRP A 212 
 HIS   0.002   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5468)
  covalent geometry    : angle       0.69750 ( 7345)
  hydrogen bonds       : bond        0.16296 (  216)
  hydrogen bonds       : angle       7.45543 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 GLN cc_start: 0.5650 (OUTLIER) cc_final: 0.5384 (mp10)
REVERT: A  201 LYS cc_start: 0.8254 (ptmm) cc_final: 0.7952 (ptmm)
REVERT: A  234 LYS cc_start: 0.7667 (mttm) cc_final: 0.7211 (mtmt)
REVERT: A  237 ASN cc_start: 0.7778 (t0) cc_final: 0.7419 (t0)
REVERT: A  266 GLU cc_start: 0.7818 (tt0) cc_final: 0.7462 (mp0)
REVERT: A  331 GLN cc_start: 0.7415 (tp40) cc_final: 0.7123 (tm130)
REVERT: B  180 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7913 (mtpp)
REVERT: B  429 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8110 (mtt)
REVERT: C  151 MET cc_start: 0.4367 (mtp) cc_final: 0.3754 (mtm)
  outliers start: 21
  outliers final: 8
  residues processed: 122
  average time/residue: 0.4080
  time to fit residues: 51.9020
Evaluate side-chains
  93 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  429 MET
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  130 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 333 GLN
A 343 ASN
B 181 ASN
B 333 ASN
B 350 ASN
B 408 GLN
C 163 ASN
** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.187029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.148459 restraints weight = 5492.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 1.75
r_work: 0.3456 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5468  Z= 0.172
  Angle     :  0.554  11.721   7345  Z= 0.289
  Chirality :  0.044   0.375    797
  Planarity :  0.004   0.041    936
  Dihedral  :  8.328  59.979    743
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 27.10 %
    Favored  : 68.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.32), residues: 639
  helix:  0.78 (0.33), residues: 236
  sheet: -1.16 (0.49), residues: 96
  loop : -0.73 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 158 
 TYR   0.011   0.001   TYR A 258 
 PHE   0.013   0.002   PHE B 148 
 TRP   0.010   0.001   TRP A 212 
 HIS   0.002   0.001   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 5468)
  covalent geometry    : angle       0.55417 ( 7345)
  hydrogen bonds       : bond        0.03754 (  216)
  hydrogen bonds       : angle       5.28714 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  150 ILE cc_start: 0.5630 (OUTLIER) cc_final: 0.5226 (mt)
REVERT: A  169 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7853 (mmm160)
REVERT: A  193 ASP cc_start: 0.6961 (t0) cc_final: 0.6317 (m-30)
REVERT: A  237 ASN cc_start: 0.8014 (t0) cc_final: 0.7613 (t0)
REVERT: B  130 LYS cc_start: 0.7068 (tttt) cc_final: 0.6726 (mttp)
REVERT: B  156 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8271 (ttmt)
REVERT: B  168 ASP cc_start: 0.7855 (m-30) cc_final: 0.7453 (m-30)
REVERT: B  180 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7769 (mttm)
REVERT: C  151 MET cc_start: 0.2118 (mtp) cc_final: 0.1844 (mtm)
REVERT: D   77 GLU cc_start: 0.6965 (tp30) cc_final: 0.6750 (tp30)
REVERT: D   91 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7836 (m)
  outliers start: 28
  outliers final: 12
  residues processed: 112
  average time/residue: 0.4285
  time to fit residues: 50.2502
Evaluate side-chains
  103 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   69 ASN
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 331 GLN
B 181 ASN
B 350 ASN
B 408 GLN
** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.187881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.148502 restraints weight = 5394.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 1.74
r_work: 0.3467 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5468  Z= 0.125
  Angle     :  0.503   9.826   7345  Z= 0.263
  Chirality :  0.042   0.356    797
  Planarity :  0.003   0.037    936
  Dihedral  :  7.106  53.304    732
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 28.28 %
    Favored  : 67.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.33), residues: 639
  helix:  1.10 (0.33), residues: 236
  sheet: -1.12 (0.53), residues: 86
  loop : -0.77 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.012   0.001   TYR A 258 
 PHE   0.010   0.001   PHE B 148 
 TRP   0.006   0.001   TRP A 212 
 HIS   0.001   0.000   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 5468)
  covalent geometry    : angle       0.50271 ( 7345)
  hydrogen bonds       : bond        0.03259 (  216)
  hydrogen bonds       : angle       4.99219 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  150 ILE cc_start: 0.5567 (OUTLIER) cc_final: 0.5099 (mt)
REVERT: A  169 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7680 (mmm-85)
REVERT: A  193 ASP cc_start: 0.6838 (t0) cc_final: 0.6318 (m-30)
REVERT: A  237 ASN cc_start: 0.7971 (t0) cc_final: 0.7613 (t0)
REVERT: B  130 LYS cc_start: 0.7024 (tttt) cc_final: 0.6696 (mmpt)
REVERT: B  137 LEU cc_start: 0.7914 (mt) cc_final: 0.7687 (mp)
REVERT: B  168 ASP cc_start: 0.7747 (m-30) cc_final: 0.7333 (m-30)
REVERT: B  180 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7853 (mttm)
REVERT: C  151 MET cc_start: 0.2135 (mtp) cc_final: 0.1867 (mtm)
REVERT: C  163 ASN cc_start: 0.7172 (m-40) cc_final: 0.6865 (m-40)
REVERT: D   77 GLU cc_start: 0.6934 (tp30) cc_final: 0.6647 (tp30)
REVERT: D   91 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7567 (m)
  outliers start: 23
  outliers final: 8
  residues processed: 111
  average time/residue: 0.4209
  time to fit residues: 48.9051
Evaluate side-chains
  92 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 331 GLN
B 350 ASN
** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.188622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.149333 restraints weight = 5475.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 1.71
r_work: 0.3435 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5468  Z= 0.114
  Angle     :  0.487  10.524   7345  Z= 0.255
  Chirality :  0.042   0.378    797
  Planarity :  0.003   0.034    936
  Dihedral  :  6.761  56.393    728
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 30.13 %
    Favored  : 66.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.33), residues: 639
  helix:  1.33 (0.33), residues: 236
  sheet: -0.98 (0.55), residues: 86
  loop : -0.68 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 378 
 TYR   0.010   0.001   TYR A 258 
 PHE   0.007   0.001   PHE B 148 
 TRP   0.005   0.001   TRP A 212 
 HIS   0.001   0.000   HIS B 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5468)
  covalent geometry    : angle       0.48691 ( 7345)
  hydrogen bonds       : bond        0.03067 (  216)
  hydrogen bonds       : angle       4.81210 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  169 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7567 (mmm-85)
REVERT: A  193 ASP cc_start: 0.6732 (t0) cc_final: 0.6200 (m-30)
REVERT: A  237 ASN cc_start: 0.7884 (t0) cc_final: 0.7504 (t0)
REVERT: B  115 LYS cc_start: 0.7900 (ttpp) cc_final: 0.7459 (tmmt)
REVERT: B  130 LYS cc_start: 0.6982 (tttt) cc_final: 0.6658 (mmpt)
REVERT: B  137 LEU cc_start: 0.7814 (mt) cc_final: 0.7578 (mp)
REVERT: B  180 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7756 (mttm)
REVERT: B  401 MET cc_start: 0.8003 (tpp) cc_final: 0.7548 (tpt)
REVERT: C  151 MET cc_start: 0.2026 (mtp) cc_final: 0.1773 (mtm)
REVERT: C  163 ASN cc_start: 0.7134 (m-40) cc_final: 0.6803 (m-40)
REVERT: D   77 GLU cc_start: 0.6995 (tp30) cc_final: 0.6671 (tp30)
REVERT: D   86 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6929 (tt0)
REVERT: D   91 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7451 (m)
  outliers start: 20
  outliers final: 11
  residues processed: 112
  average time/residue: 0.4609
  time to fit residues: 54.1732
Evaluate side-chains
  103 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   69 ASN
Chi-restraints excluded: chain D residue   86 GLU
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0970
   chunk 36 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
A 296 GLN
A 331 GLN
B 171 ASN
B 350 ASN
** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.187916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.148586 restraints weight = 5608.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.72
r_work: 0.3447 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5468  Z= 0.119
  Angle     :  0.492   9.100   7345  Z= 0.258
  Chirality :  0.042   0.315    797
  Planarity :  0.003   0.034    936
  Dihedral  :  6.853  59.161    728
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 27.61 %
    Favored  : 67.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.33), residues: 639
  helix:  1.48 (0.34), residues: 236
  sheet: -0.92 (0.56), residues: 85
  loop : -0.62 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.011   0.001   TYR A 258 
 PHE   0.008   0.001   PHE D  42 
 TRP   0.005   0.001   TRP A 212 
 HIS   0.001   0.000   HIS B 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5468)
  covalent geometry    : angle       0.49241 ( 7345)
  hydrogen bonds       : bond        0.02987 (  216)
  hydrogen bonds       : angle       4.66682 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7571 (mmm160)
REVERT: A  193 ASP cc_start: 0.6734 (t0) cc_final: 0.6331 (m-30)
REVERT: A  237 ASN cc_start: 0.7987 (t0) cc_final: 0.7643 (t0)
REVERT: A  266 GLU cc_start: 0.8112 (tt0) cc_final: 0.7669 (tp30)
REVERT: B  115 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7517 (tmmt)
REVERT: B  130 LYS cc_start: 0.7076 (tttt) cc_final: 0.6756 (mmpt)
REVERT: B  137 LEU cc_start: 0.7972 (mt) cc_final: 0.7735 (mp)
REVERT: B  180 LYS cc_start: 0.8092 (ttmm) cc_final: 0.7777 (mttm)
REVERT: B  323 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6612 (tt0)
REVERT: B  401 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7717 (ttp)
REVERT: C  151 MET cc_start: 0.2109 (mtp) cc_final: 0.1787 (ptp)
REVERT: C  163 ASN cc_start: 0.7185 (m-40) cc_final: 0.6887 (m-40)
REVERT: D   77 GLU cc_start: 0.6894 (tp30) cc_final: 0.6586 (tp30)
REVERT: D   86 GLU cc_start: 0.7312 (tt0) cc_final: 0.7079 (tt0)
REVERT: D   91 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7541 (m)
  outliers start: 29
  outliers final: 13
  residues processed: 113
  average time/residue: 0.4690
  time to fit residues: 55.2787
Evaluate side-chains
  99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LYS
Chi-restraints excluded: chain A residue  246 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  323 GLN
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   69 ASN
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  123 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 40 optimal weight:    0.0040
   chunk 51 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 331 GLN
B 171 ASN
B 181 ASN
B 202 GLN
B 350 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.183290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.139063 restraints weight = 5536.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 1.86
r_work: 0.3521 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5468  Z= 0.116
  Angle     :  0.504   9.377   7345  Z= 0.262
  Chirality :  0.042   0.335    797
  Planarity :  0.003   0.034    936
  Dihedral  :  6.766  59.087    728
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 28.62 %
    Favored  : 67.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.33), residues: 639
  helix:  1.61 (0.34), residues: 236
  sheet: -0.81 (0.57), residues: 84
  loop : -0.52 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 259 
 TYR   0.010   0.001   TYR A 258 
 PHE   0.007   0.001   PHE D  42 
 TRP   0.005   0.001   TRP A 212 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5468)
  covalent geometry    : angle       0.50397 ( 7345)
  hydrogen bonds       : bond        0.02979 (  216)
  hydrogen bonds       : angle       4.67764 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  169 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7613 (mmm160)
REVERT: A  193 ASP cc_start: 0.6682 (t0) cc_final: 0.6324 (m-30)
REVERT: A  237 ASN cc_start: 0.7983 (t0) cc_final: 0.7693 (t0)
REVERT: A  266 GLU cc_start: 0.8204 (tt0) cc_final: 0.7747 (tp30)
REVERT: B  115 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7584 (tmmt)
REVERT: B  130 LYS cc_start: 0.7130 (tttt) cc_final: 0.6868 (mmpt)
REVERT: B  137 LEU cc_start: 0.8075 (mt) cc_final: 0.7837 (mp)
REVERT: B  180 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7810 (mttm)
REVERT: B  384 ASP cc_start: 0.8308 (t70) cc_final: 0.7888 (t0)
REVERT: B  401 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7731 (ttp)
REVERT: C  151 MET cc_start: 0.2460 (mtp) cc_final: 0.2162 (ptp)
REVERT: C  163 ASN cc_start: 0.7363 (m-40) cc_final: 0.7057 (m-40)
REVERT: D   77 GLU cc_start: 0.6945 (tp30) cc_final: 0.6580 (tp30)
REVERT: D   86 GLU cc_start: 0.7644 (tt0) cc_final: 0.7392 (tt0)
REVERT: D   91 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7717 (m)
  outliers start: 23
  outliers final: 12
  residues processed: 102
  average time/residue: 0.4029
  time to fit residues: 43.1383
Evaluate side-chains
  100 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LYS
Chi-restraints excluded: chain A residue  246 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   69 ASN
Chi-restraints excluded: chain D residue   91 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 62 optimal weight:   20.0000
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 42 optimal weight:    0.4980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 331 GLN
B 171 ASN
B 181 ASN
B 350 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.182847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.138675 restraints weight = 5574.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.85
r_work: 0.3513 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5468  Z= 0.123
  Angle     :  0.503   8.026   7345  Z= 0.262
  Chirality :  0.041   0.272    797
  Planarity :  0.003   0.034    936
  Dihedral  :  6.814  58.759    728
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 27.61 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.33), residues: 639
  helix:  1.68 (0.34), residues: 236
  sheet: -0.84 (0.57), residues: 85
  loop : -0.61 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 259 
 TYR   0.011   0.001   TYR A 258 
 PHE   0.007   0.001   PHE D  42 
 TRP   0.006   0.001   TRP A 212 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5468)
  covalent geometry    : angle       0.50306 ( 7345)
  hydrogen bonds       : bond        0.03001 (  216)
  hydrogen bonds       : angle       4.64840 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7611 (mmm160)
REVERT: A  193 ASP cc_start: 0.6739 (t0) cc_final: 0.6383 (m-30)
REVERT: A  237 ASN cc_start: 0.7987 (t0) cc_final: 0.7704 (t0)
REVERT: A  266 GLU cc_start: 0.8204 (tt0) cc_final: 0.7757 (tp30)
REVERT: B  101 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7453 (mp)
REVERT: B  115 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7604 (tmmt)
REVERT: B  130 LYS cc_start: 0.7164 (tttt) cc_final: 0.6935 (mmpt)
REVERT: B  137 LEU cc_start: 0.8128 (mt) cc_final: 0.7899 (mp)
REVERT: B  180 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7813 (mttm)
REVERT: B  323 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6870 (tt0)
REVERT: B  401 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7734 (ttp)
REVERT: B  426 HIS cc_start: 0.6516 (p-80) cc_final: 0.5969 (p-80)
REVERT: C  151 MET cc_start: 0.2616 (mtp) cc_final: 0.2322 (ptp)
REVERT: D   19 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7482 (mttm)
REVERT: D   77 GLU cc_start: 0.6953 (tp30) cc_final: 0.6646 (tp30)
REVERT: D   91 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7760 (m)
  outliers start: 28
  outliers final: 14
  residues processed: 116
  average time/residue: 0.4575
  time to fit residues: 55.5914
Evaluate side-chains
  104 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LYS
Chi-restraints excluded: chain A residue  246 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  323 GLN
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   69 ASN
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  123 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0980
   chunk 1 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
A 296 GLN
A 331 GLN
B 171 ASN
B 181 ASN
B 350 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.174784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.133514 restraints weight = 5536.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.82
r_work: 0.3337 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5468  Z= 0.173
  Angle     :  0.569  11.558   7345  Z= 0.291
  Chirality :  0.046   0.498    797
  Planarity :  0.004   0.034    936
  Dihedral  :  7.024  59.471    728
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 28.62 %
    Favored  : 67.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.33), residues: 639
  helix:  1.54 (0.33), residues: 236
  sheet: -0.97 (0.56), residues: 86
  loop : -0.61 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 259 
 TYR   0.014   0.002   TYR C 171 
 PHE   0.013   0.001   PHE A 203 
 TRP   0.011   0.001   TRP A 212 
 HIS   0.002   0.001   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 5468)
  covalent geometry    : angle       0.56893 ( 7345)
  hydrogen bonds       : bond        0.03317 (  216)
  hydrogen bonds       : angle       4.80486 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7465 (mmm160)
REVERT: A  193 ASP cc_start: 0.6795 (t0) cc_final: 0.6249 (m-30)
REVERT: A  237 ASN cc_start: 0.7979 (t0) cc_final: 0.7629 (t0)
REVERT: A  245 GLN cc_start: 0.7694 (mp10) cc_final: 0.7392 (mm110)
REVERT: A  266 GLU cc_start: 0.8128 (tt0) cc_final: 0.7471 (tp30)
REVERT: B  115 LYS cc_start: 0.7926 (ttpp) cc_final: 0.7459 (tmmt)
REVERT: B  130 LYS cc_start: 0.7023 (tttt) cc_final: 0.6678 (mmpt)
REVERT: B  137 LEU cc_start: 0.7920 (mt) cc_final: 0.7695 (mp)
REVERT: B  168 ASP cc_start: 0.7794 (m-30) cc_final: 0.7351 (m-30)
REVERT: B  180 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7854 (mttm)
REVERT: B  198 GLU cc_start: 0.7355 (tt0) cc_final: 0.6952 (mt-10)
REVERT: B  323 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6466 (tt0)
REVERT: B  401 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7799 (ttp)
REVERT: B  426 HIS cc_start: 0.6310 (p-80) cc_final: 0.5662 (p-80)
REVERT: C  151 MET cc_start: 0.2253 (mtp) cc_final: 0.1999 (ptp)
REVERT: D   77 GLU cc_start: 0.6756 (tp30) cc_final: 0.6352 (tp30)
REVERT: D   91 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7464 (m)
  outliers start: 25
  outliers final: 15
  residues processed: 115
  average time/residue: 0.5393
  time to fit residues: 64.6251
Evaluate side-chains
  108 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  246 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  323 GLN
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   69 ASN
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  123 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 62 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 38 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 331 GLN
B 171 ASN
B 181 ASN
B 350 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.176011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135129 restraints weight = 5573.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 1.83
r_work: 0.3390 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5468  Z= 0.132
  Angle     :  0.542  13.540   7345  Z= 0.275
  Chirality :  0.044   0.514    797
  Planarity :  0.003   0.033    936
  Dihedral  :  6.842  59.057    728
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 28.62 %
    Favored  : 67.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.33), residues: 639
  helix:  1.66 (0.34), residues: 236
  sheet: -1.07 (0.56), residues: 86
  loop : -0.59 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 259 
 TYR   0.021   0.001   TYR B 407 
 PHE   0.009   0.001   PHE D  42 
 TRP   0.006   0.001   TRP A 212 
 HIS   0.001   0.000   HIS B 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5468)
  covalent geometry    : angle       0.54200 ( 7345)
  hydrogen bonds       : bond        0.03107 (  216)
  hydrogen bonds       : angle       4.76028 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7544 (mmm160)
REVERT: A  237 ASN cc_start: 0.8020 (t0) cc_final: 0.7694 (t0)
REVERT: A  245 GLN cc_start: 0.7666 (mp10) cc_final: 0.7377 (mm110)
REVERT: A  266 GLU cc_start: 0.8204 (tt0) cc_final: 0.7623 (tp30)
REVERT: B  115 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7534 (tmmt)
REVERT: B  130 LYS cc_start: 0.7092 (tttt) cc_final: 0.6811 (mmpt)
REVERT: B  137 LEU cc_start: 0.8023 (mt) cc_final: 0.7791 (mp)
REVERT: B  168 ASP cc_start: 0.7850 (m-30) cc_final: 0.7443 (m-30)
REVERT: B  180 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7807 (mttm)
REVERT: B  323 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6690 (tt0)
REVERT: B  401 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7618 (tpt)
REVERT: B  426 HIS cc_start: 0.6444 (p-80) cc_final: 0.5864 (p-80)
REVERT: C  151 MET cc_start: 0.2330 (mtp) cc_final: 0.2071 (ptp)
REVERT: D   77 GLU cc_start: 0.6889 (tp30) cc_final: 0.6475 (tp30)
REVERT: D   91 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7526 (p)
  outliers start: 25
  outliers final: 12
  residues processed: 113
  average time/residue: 0.4225
  time to fit residues: 50.0115
Evaluate side-chains
  104 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  323 GLN
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  123 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 48 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 331 GLN
B 171 ASN
B 181 ASN
B 350 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.176801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.136097 restraints weight = 5623.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.81
r_work: 0.3490 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5468  Z= 0.134
  Angle     :  0.544  12.757   7345  Z= 0.277
  Chirality :  0.043   0.411    797
  Planarity :  0.003   0.033    936
  Dihedral  :  6.804  59.869    728
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 30.13 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.33), residues: 639
  helix:  1.67 (0.34), residues: 236
  sheet: -0.93 (0.57), residues: 84
  loop : -0.53 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 259 
 TYR   0.016   0.001   TYR C 171 
 PHE   0.009   0.001   PHE D  42 
 TRP   0.006   0.001   TRP A 212 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5468)
  covalent geometry    : angle       0.54421 ( 7345)
  hydrogen bonds       : bond        0.03125 (  216)
  hydrogen bonds       : angle       4.74463 (  594)

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7603 (mmm160)
REVERT: A  193 ASP cc_start: 0.6780 (t0) cc_final: 0.6393 (m-30)
REVERT: A  237 ASN cc_start: 0.7955 (t0) cc_final: 0.7680 (t0)
REVERT: A  245 GLN cc_start: 0.7580 (mp10) cc_final: 0.7315 (mm110)
REVERT: A  266 GLU cc_start: 0.8245 (tt0) cc_final: 0.7740 (tp30)
REVERT: B  101 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7387 (mp)
REVERT: B  115 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7633 (tmmt)
REVERT: B  130 LYS cc_start: 0.7170 (tttt) cc_final: 0.6952 (mmpt)
REVERT: B  137 LEU cc_start: 0.8106 (mt) cc_final: 0.7880 (mp)
REVERT: B  168 ASP cc_start: 0.7831 (m-30) cc_final: 0.7446 (m-30)
REVERT: B  180 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7849 (mttm)
REVERT: B  198 GLU cc_start: 0.7496 (tt0) cc_final: 0.7202 (mt-10)
REVERT: B  323 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6819 (tt0)
REVERT: B  401 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7722 (ttp)
REVERT: B  426 HIS cc_start: 0.6559 (p-80) cc_final: 0.6030 (p-80)
REVERT: C  151 MET cc_start: 0.2708 (mtp) cc_final: 0.2357 (ptp)
REVERT: D   77 GLU cc_start: 0.6979 (tp30) cc_final: 0.6598 (tp30)
REVERT: D   91 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7679 (p)
  outliers start: 17
  outliers final: 11
  residues processed: 110
  average time/residue: 0.4872
  time to fit residues: 55.8863
Evaluate side-chains
  106 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  323 GLN
Chi-restraints excluded: chain B residue  329 LYS
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  123 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 54 optimal weight:    0.0050
   chunk 8 optimal weight:    0.0970
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0570
   chunk 25 optimal weight:    8.9990
   overall best weight:    0.2110

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 331 GLN
B 131 ASN
B 181 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.191028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.149290 restraints weight = 5592.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 1.77
r_work: 0.3604 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5468  Z= 0.093
  Angle     :  0.514  13.694   7345  Z= 0.260
  Chirality :  0.042   0.459    797
  Planarity :  0.003   0.034    936
  Dihedral  :  6.415  57.912    728
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 30.47 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.34), residues: 639
  helix:  1.84 (0.34), residues: 236
  sheet: -1.01 (0.56), residues: 86
  loop : -0.50 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 259 
 TYR   0.015   0.001   TYR B 407 
 PHE   0.008   0.001   PHE D  42 
 TRP   0.006   0.001   TRP D  70 
 HIS   0.002   0.000   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 5468)
  covalent geometry    : angle       0.51350 ( 7345)
  hydrogen bonds       : bond        0.02818 (  216)
  hydrogen bonds       : angle       4.59963 (  594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2161.90 seconds
wall clock time: 37 minutes 25.49 seconds (2245.49 seconds total)