Starting phenix.real_space_refine
on Tue Feb  3 16:50:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v0t_64671/02_2026/9v0t_64671.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v0t_64671/02_2026/9v0t_64671.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v0t_64671/02_2026/9v0t_64671.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v0t_64671/02_2026/9v0t_64671.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v0t_64671/02_2026/9v0t_64671.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v0t_64671/02_2026/9v0t_64671.cif"
  }
  resolution = 4.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.039
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      29      5.16       5
     C    3192      2.51       5
     N     875      2.21       5
     O     994      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  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: 5090
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "D"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 908
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "E"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 827
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 101}
    Chain: "F"
      Number of atoms: 3355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3355
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 14, 'TRANS': 427}
          Chain breaks: 1
  Time building chain proxies: 1.21, per 1000 atoms: 0.24
  Number of scatterers: 5090
  At special positions: 0
  Unit cell: (70.448, 114.996, 97.384, 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      29     16.00
     O     994      8.00
     N     875      7.00
     C    3192      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  28 " - pdb=" SG  CYS F 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  60 " - pdb=" SG  CYS F 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 283 " - pdb=" SG  CYS F 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 292 " - pdb=" SG  CYS F 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 326 " - pdb=" SG  CYS F 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 384 " - pdb=" SG  CYS F 390 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 258.3 milliseconds
  

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1226

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 8 sheets defined
      24.1% alpha, 24.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'D' and resid 62 through 65
      removed outlier: 3.641A  pdb=" N   LYS D  65 " --> pdb=" O   ASP D  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 62 through 65'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.793A  pdb=" N   THR D  91 " --> pdb=" O   VAL D  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 54 through 58
    Processing helix  chain 'F' and resid 65 through 81
    Processing helix  chain 'F' and resid 104 through 109
    Processing helix  chain 'F' and resid 111 through 129
      removed outlier: 3.501A  pdb=" N   ALA F 115 " --> pdb=" O   GLY F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 130 through 142
      removed outlier: 3.577A  pdb=" N   LYS F 142 " --> pdb=" O   LYS F 138 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 163 through 172
    Processing helix  chain 'F' and resid 172 through 177
    Processing helix  chain 'F' and resid 186 through 210
      removed outlier: 3.929A  pdb=" N   ALA F 190 " --> pdb=" O   ASP F 186 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   ARG F 199 " --> pdb=" O   GLN F 195 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   PHE F 200 " --> pdb=" O   PHE F 196 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 223 through 233
    Processing helix  chain 'F' and resid 237 through 247
    Processing helix  chain 'F' and resid 247 through 255
      removed outlier: 3.707A  pdb=" N   VAL F 251 " --> pdb=" O   ASN F 247 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 344 through 351
      removed outlier: 3.812A  pdb=" N   SER F 347 " --> pdb=" O   ALA F 344 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 460 through 472
    Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7
    Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 60
      removed outlier: 5.305A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.201A  pdb=" N   VAL E  10 " --> pdb=" O   LYS E 106 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   THR E 108 " --> pdb=" O   VAL E  10 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY E  12 " --> pdb=" O   THR E 108 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   GLN E  39 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   VAL E  48 " --> pdb=" O   GLN E  39 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 18 through 23
    Processing sheet with id=AA5, first strand: chain 'F' and resid 20 through 24
      removed outlier: 8.827A  pdb=" N   THR F 160 " --> pdb=" O   THR F  45 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   VAL F  47 " --> pdb=" O   THR F 160 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   VAL F 162 " --> pdb=" O   VAL F  47 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   THR F  49 " --> pdb=" O   VAL F 162 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 160 through 162
    current: chain 'F' and resid 266 through 288
      removed outlier: 4.065A  pdb=" N   GLN F 312 " --> pdb=" O   PRO F 282 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 316 through 320
    current: chain 'F' and resid 332 through 336
    Processing sheet with id=AA6, first strand: chain 'F' and resid 291 through 295
      removed outlier: 7.287A  pdb=" N   THR F 365 " --> pdb=" O   PHE F 456 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   PHE F 456 " --> pdb=" O   THR F 365 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 374 through 375
    Processing sheet with id=AA8, first strand: chain 'F' and resid 399 through 402
      removed outlier: 3.906A  pdb=" N   LYS F 401 " --> pdb=" O   ILE F 392 " (cutoff:3.500A)

    192 hydrogen bonds defined for protein.
    492 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: 0.72

  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 -     1.35: 1685
        1.35 -     1.47: 1210
        1.47 -     1.59: 2244
        1.59 -     1.72: 0
        1.72 -     1.84: 40
  Bond restraints: 5179
  Sorted by residual:
  bond pdb=" CA  ASN D  56 "
       pdb=" CB  ASN D  56 "
    ideal  model  delta    sigma   weight residual
    1.530  1.559 -0.029 1.69e-02 3.50e+03 2.97e+00
  bond pdb=" C   GLN E  81 "
       pdb=" N   PRO E  82 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.19e-02 7.06e+03 2.34e+00
  bond pdb=" CA  GLU E  52 "
       pdb=" C   GLU E  52 "
    ideal  model  delta    sigma   weight residual
    1.524  1.546 -0.022 1.57e-02 4.06e+03 2.00e+00
  bond pdb=" CA  ILE F 279 "
       pdb=" CB  ILE F 279 "
    ideal  model  delta    sigma   weight residual
    1.544  1.562 -0.018 1.42e-02 4.96e+03 1.57e+00
  bond pdb=" CB  VAL D  97 "
       pdb=" CG2 VAL D  97 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.37e+00
  ... (remaining 5174 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 6822
        2.54 -     5.08: 163
        5.08 -     7.62: 30
        7.62 -    10.16: 7
       10.16 -    12.70: 1
  Bond angle restraints: 7023
  Sorted by residual:
  angle pdb=" N   VAL D 103 "
        pdb=" CA  VAL D 103 "
        pdb=" C   VAL D 103 "
      ideal   model   delta    sigma   weight residual
     112.29  107.62    4.67 9.40e-01 1.13e+00 2.47e+01
  angle pdb=" C   GLU E  52 "
        pdb=" N   ASN E  53 "
        pdb=" CA  ASN E  53 "
      ideal   model   delta    sigma   weight residual
     121.54  129.66   -8.12 1.91e+00 2.74e-01 1.81e+01
  angle pdb=" CB  MET F 244 "
        pdb=" CG  MET F 244 "
        pdb=" SD  MET F 244 "
      ideal   model   delta    sigma   weight residual
     112.70  125.40  -12.70 3.00e+00 1.11e-01 1.79e+01
  angle pdb=" N   GLY D  55 "
        pdb=" CA  GLY D  55 "
        pdb=" C   GLY D  55 "
      ideal   model   delta    sigma   weight residual
     113.18  122.82   -9.64 2.37e+00 1.78e-01 1.65e+01
  angle pdb=" C   GLY D  55 "
        pdb=" N   ASN D  56 "
        pdb=" CA  ASN D  56 "
      ideal   model   delta    sigma   weight residual
     121.54  113.83    7.71 1.91e+00 2.74e-01 1.63e+01
  ... (remaining 7018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 2828
       17.08 -    34.16: 242
       34.16 -    51.24: 46
       51.24 -    68.31: 7
       68.31 -    85.39: 2
  Dihedral angle restraints: 3125
    sinusoidal: 1207
      harmonic: 1918
  Sorted by residual:
  dihedral pdb=" CB  CYS F 384 "
           pdb=" SG  CYS F 384 "
           pdb=" SG  CYS F 390 "
           pdb=" CB  CYS F 390 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.39  -85.39     1      1.00e+01 1.00e-02 8.83e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  90 "
           pdb=" CB  CYS E  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.20  -63.20     1      1.00e+01 1.00e-02 5.27e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  96 "
           pdb=" CB  CYS D  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.21  -55.21     1      1.00e+01 1.00e-02 4.12e+01
  ... (remaining 3122 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 581
       0.050 -    0.101: 185
       0.101 -    0.151: 37
       0.151 -    0.202: 6
       0.202 -    0.252: 1
  Chirality restraints: 810
  Sorted by residual:
  chirality pdb=" CB  ILE F 420 "
            pdb=" CA  ILE F 420 "
            pdb=" CG1 ILE F 420 "
            pdb=" CG2 ILE F 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CG  LEU F 158 "
            pdb=" CB  LEU F 158 "
            pdb=" CD1 LEU F 158 "
            pdb=" CD2 LEU F 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.18 2.00e-01 2.50e+01 8.55e-01
  chirality pdb=" CB  ILE F  31 "
            pdb=" CA  ILE F  31 "
            pdb=" CG1 ILE F  31 "
            pdb=" CG2 ILE F  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.31e-01
  ... (remaining 807 not shown)

  Planarity restraints: 904
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E  37 "    0.020 2.00e-02 2.50e+03   1.93e-02 9.33e+00
        pdb=" CG  TRP E  37 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP E  37 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP E  37 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP E  37 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP E  37 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP E  37 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E  37 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E  37 "    0.015 2.00e-02 2.50e+03
        pdb=" CH2 TRP E  37 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E  81 "   -0.041 5.00e-02 4.00e+02   6.35e-02 6.46e+00
        pdb=" N   PRO E  82 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO E  82 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E  82 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F 281 "    0.035 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO F 282 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO F 282 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO F 282 "    0.029 5.00e-02 4.00e+02
  ... (remaining 901 not shown)

  Histogram of nonbonded interaction distances:
        2.58 -     3.05: 3015
        3.05 -     3.51: 5347
        3.51 -     3.97: 8101
        3.97 -     4.44: 8965
        4.44 -     4.90: 14456
  Nonbonded interactions: 39884
  Sorted by model distance:
  nonbonded pdb=" N   VAL D 103 "
            pdb=" N   MET D 104 "
     model   vdw
     2.584 2.560
  nonbonded pdb=" O   GLY D  55 "
            pdb=" CA  ASN D  56 "
     model   vdw
     2.590 2.776
  nonbonded pdb=" O   TYR E  93 "
            pdb=" CB  TYR E  93 "
     model   vdw
     2.592 2.752
  nonbonded pdb=" N   SER E  11 "
            pdb=" O   SER E  11 "
     model   vdw
     2.596 2.496
  nonbonded pdb=" O   ALA F 249 "
            pdb=" CA  MET F 250 "
     model   vdw
     2.612 2.776
  ... (remaining 39879 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.710
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
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   0.039   5188  Z= 0.195
  Angle     :  0.963  12.701   7041  Z= 0.508
  Chirality :  0.051   0.252    810
  Planarity :  0.006   0.064    904
  Dihedral  : 12.867  73.838   1872
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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: -1.35 (0.31), residues: 665
  helix: -1.15 (0.39), residues: 144
  sheet: -0.01 (0.38), residues: 183
  loop : -1.24 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  76 
 TYR   0.019   0.002   TYR E  93 
 PHE   0.026   0.002   PHE F 207 
 TRP   0.049   0.004   TRP E  37 
 HIS   0.006   0.001   HIS E  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5179)
  covalent geometry    : angle       0.96200 ( 7023)
  SS BOND              : bond        0.00583 (    9)
  SS BOND              : angle       1.36866 (   18)
  hydrogen bonds       : bond        0.09417 (  192)
  hydrogen bonds       : angle       6.04678 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   47 TRP cc_start: 0.8685 (t60) cc_final: 0.7501 (t60)
REVERT: D   57 TYR cc_start: 0.8935 (m-10) cc_final: 0.8646 (m-10)
REVERT: D  108 TRP cc_start: 0.8972 (p90) cc_final: 0.8646 (p90)
REVERT: D  110 ASP cc_start: 0.8582 (p0) cc_final: 0.8362 (p0)
REVERT: E   34 ASP cc_start: 0.7438 (p0) cc_final: 0.6383 (p0)
REVERT: E   36 HIS cc_start: 0.6887 (m170) cc_final: 0.5646 (m170)
REVERT: E   38 TYR cc_start: 0.8317 (m-80) cc_final: 0.7968 (m-80)
REVERT: E   89 TYR cc_start: 0.8776 (m-80) cc_final: 0.8405 (m-80)
REVERT: E  107 LEU cc_start: 0.8261 (tp) cc_final: 0.8034 (tp)
REVERT: F   39 LEU cc_start: 0.9513 (mp) cc_final: 0.9193 (mp)
REVERT: F  193 PHE cc_start: 0.9147 (t80) cc_final: 0.8809 (t80)
REVERT: F  202 ASN cc_start: 0.9370 (t0) cc_final: 0.9024 (t0)
REVERT: F  278 VAL cc_start: 0.8948 (t) cc_final: 0.8162 (t)
REVERT: F  359 TYR cc_start: 0.8323 (t80) cc_final: 0.7862 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0561
  time to fit residues: 8.1126
Evaluate side-chains
  78 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 298 ASN
** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.083114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.061302 restraints weight = 20764.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.063406 restraints weight = 12012.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.064917 restraints weight = 8420.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.065904 restraints weight = 6595.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.066367 restraints weight = 5601.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.126   5188  Z= 0.277
  Angle     :  0.697   9.306   7041  Z= 0.370
  Chirality :  0.042   0.151    810
  Planarity :  0.005   0.049    904
  Dihedral  :  5.805  47.043    724
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 17.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  6.21 %
    Favored  : 93.62 %
  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: -1.03 (0.32), residues: 665
  helix:  0.24 (0.45), residues: 140
  sheet: -0.43 (0.35), residues: 211
  loop : -1.22 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  72 
 TYR   0.016   0.002   TYR F 320 
 PHE   0.009   0.002   PHE F 276 
 TRP   0.017   0.003   TRP E  99 
 HIS   0.003   0.001   HIS F 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00622 ( 5179)
  covalent geometry    : angle       0.69593 ( 7023)
  SS BOND              : bond        0.00481 (    9)
  SS BOND              : angle       1.06769 (   18)
  hydrogen bonds       : bond        0.04205 (  192)
  hydrogen bonds       : angle       5.31709 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: D   47 TRP cc_start: 0.8814 (t60) cc_final: 0.8077 (t60)
REVERT: D   87 ARG cc_start: 0.8900 (pmt-80) cc_final: 0.8415 (pmt-80)
REVERT: E   36 HIS cc_start: 0.6657 (m170) cc_final: 0.6234 (m170)
REVERT: E   85 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6845 (mm-30)
REVERT: E  101 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7783 (m-10)
REVERT: E  106 LYS cc_start: 0.8018 (tptp) cc_final: 0.7495 (tptp)
REVERT: E  107 LEU cc_start: 0.8452 (tp) cc_final: 0.8007 (tp)
REVERT: F   39 LEU cc_start: 0.9625 (mp) cc_final: 0.9282 (mp)
REVERT: F  193 PHE cc_start: 0.9218 (t80) cc_final: 0.8770 (t80)
REVERT: F  202 ASN cc_start: 0.9363 (t0) cc_final: 0.9060 (t0)
REVERT: F  205 ARG cc_start: 0.9131 (ptp-110) cc_final: 0.8859 (ptm-80)
REVERT: F  270 MET cc_start: 0.9147 (ppp) cc_final: 0.8687 (ppp)
REVERT: F  278 VAL cc_start: 0.9321 (t) cc_final: 0.8509 (t)
REVERT: F  359 TYR cc_start: 0.8392 (t80) cc_final: 0.7881 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0611
  time to fit residues: 7.1527
Evaluate side-chains
  68 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0570
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 298 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.087887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.066698 restraints weight = 19818.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.069018 restraints weight = 11409.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.070589 restraints weight = 7880.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.071699 restraints weight = 6089.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.072453 restraints weight = 5101.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5188  Z= 0.105
  Angle     :  0.609   8.792   7041  Z= 0.310
  Chirality :  0.042   0.157    810
  Planarity :  0.004   0.045    904
  Dihedral  :  5.100  42.413    724
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  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: -0.70 (0.33), residues: 665
  helix:  0.71 (0.45), residues: 145
  sheet: -0.19 (0.38), residues: 182
  loop : -1.12 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  76 
 TYR   0.012   0.001   TYR E  93 
 PHE   0.015   0.001   PHE F 207 
 TRP   0.011   0.001   TRP E  37 
 HIS   0.004   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 5179)
  covalent geometry    : angle       0.60888 ( 7023)
  SS BOND              : bond        0.00446 (    9)
  SS BOND              : angle       0.80569 (   18)
  hydrogen bonds       : bond        0.03198 (  192)
  hydrogen bonds       : angle       4.59176 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   47 TRP cc_start: 0.8632 (t60) cc_final: 0.7647 (t60)
REVERT: D   56 ASN cc_start: 0.8396 (p0) cc_final: 0.8178 (p0)
REVERT: D   57 TYR cc_start: 0.8905 (m-10) cc_final: 0.8348 (m-10)
REVERT: D   76 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8445 (ttp-110)
REVERT: E   36 HIS cc_start: 0.6530 (m170) cc_final: 0.6087 (m170)
REVERT: E   38 TYR cc_start: 0.8006 (m-80) cc_final: 0.7799 (m-80)
REVERT: E   85 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7191 (mm-30)
REVERT: E  107 LEU cc_start: 0.8244 (tp) cc_final: 0.7962 (tp)
REVERT: F   39 LEU cc_start: 0.9545 (mp) cc_final: 0.9237 (mp)
REVERT: F  193 PHE cc_start: 0.9162 (t80) cc_final: 0.8765 (t80)
REVERT: F  202 ASN cc_start: 0.9366 (t0) cc_final: 0.9028 (t0)
REVERT: F  278 VAL cc_start: 0.9188 (t) cc_final: 0.8463 (t)
REVERT: F  359 TYR cc_start: 0.8222 (t80) cc_final: 0.7783 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0651
  time to fit residues: 8.7667
Evaluate side-chains
  79 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   chunk 5 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
D 114 GLN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.086802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.065322 restraints weight = 20185.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.067509 restraints weight = 11659.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.069124 restraints weight = 8150.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.070211 restraints weight = 6336.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.070931 restraints weight = 5337.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5188  Z= 0.124
  Angle     :  0.607   8.033   7041  Z= 0.310
  Chirality :  0.041   0.136    810
  Planarity :  0.003   0.034    904
  Dihedral  :  4.983  43.606    724
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  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: -0.64 (0.33), residues: 665
  helix:  0.93 (0.46), residues: 145
  sheet: -0.21 (0.38), residues: 182
  loop : -1.13 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  87 
 TYR   0.012   0.001   TYR E  89 
 PHE   0.012   0.001   PHE F 207 
 TRP   0.014   0.001   TRP E  37 
 HIS   0.004   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5179)
  covalent geometry    : angle       0.60612 ( 7023)
  SS BOND              : bond        0.00308 (    9)
  SS BOND              : angle       0.78592 (   18)
  hydrogen bonds       : bond        0.03277 (  192)
  hydrogen bonds       : angle       4.52194 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.201 
Fit side-chains
REVERT: D   47 TRP cc_start: 0.8746 (t60) cc_final: 0.7759 (t60)
REVERT: D  104 MET cc_start: 0.8287 (ttm) cc_final: 0.8024 (ttp)
REVERT: E   36 HIS cc_start: 0.6804 (m170) cc_final: 0.6193 (m90)
REVERT: E   82 PRO cc_start: 0.8610 (Cg_exo) cc_final: 0.8403 (Cg_endo)
REVERT: E   85 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7149 (mm-30)
REVERT: E  107 LEU cc_start: 0.8287 (tp) cc_final: 0.7985 (tp)
REVERT: F   39 LEU cc_start: 0.9558 (mp) cc_final: 0.9242 (mp)
REVERT: F  193 PHE cc_start: 0.9219 (t80) cc_final: 0.8812 (t80)
REVERT: F  202 ASN cc_start: 0.9348 (t0) cc_final: 0.8946 (t0)
REVERT: F  205 ARG cc_start: 0.9082 (ptp-110) cc_final: 0.8794 (ptm-80)
REVERT: F  278 VAL cc_start: 0.9158 (t) cc_final: 0.8407 (t)
REVERT: F  359 TYR cc_start: 0.8221 (t80) cc_final: 0.7669 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0645
  time to fit residues: 8.3639
Evaluate side-chains
  74 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 59 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0670
   chunk 1 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.2924

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

Flipped N/Q/H residues before XYZ refinement:
D  56 ASN
D  74 ASN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.086464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.064713 restraints weight = 20648.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.066955 restraints weight = 11920.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.068489 restraints weight = 8323.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.069590 restraints weight = 6507.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.070304 restraints weight = 5507.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5188  Z= 0.131
  Angle     :  0.601   8.102   7041  Z= 0.308
  Chirality :  0.041   0.131    810
  Planarity :  0.003   0.033    904
  Dihedral  :  4.933  43.912    724
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.19 %
    Favored  : 96.63 %
  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: -0.57 (0.33), residues: 665
  helix:  1.03 (0.47), residues: 145
  sheet: -0.23 (0.38), residues: 182
  loop : -1.07 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  76 
 TYR   0.008   0.001   TYR E  93 
 PHE   0.008   0.001   PHE F 207 
 TRP   0.017   0.001   TRP E  37 
 HIS   0.003   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5179)
  covalent geometry    : angle       0.59994 ( 7023)
  SS BOND              : bond        0.00339 (    9)
  SS BOND              : angle       0.80982 (   18)
  hydrogen bonds       : bond        0.03078 (  192)
  hydrogen bonds       : angle       4.40693 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: D   47 TRP cc_start: 0.8759 (t60) cc_final: 0.7789 (t60)
REVERT: D   57 TYR cc_start: 0.8868 (m-10) cc_final: 0.8032 (m-10)
REVERT: D   87 ARG cc_start: 0.8863 (pmt-80) cc_final: 0.8266 (pmt-80)
REVERT: E   36 HIS cc_start: 0.7047 (m170) cc_final: 0.6439 (m90)
REVERT: E   38 TYR cc_start: 0.7899 (m-80) cc_final: 0.7602 (m-80)
REVERT: E  107 LEU cc_start: 0.8327 (tp) cc_final: 0.7846 (tp)
REVERT: F   39 LEU cc_start: 0.9575 (mp) cc_final: 0.9140 (mp)
REVERT: F  193 PHE cc_start: 0.9237 (t80) cc_final: 0.8834 (t80)
REVERT: F  202 ASN cc_start: 0.9388 (t0) cc_final: 0.9088 (t0)
REVERT: F  205 ARG cc_start: 0.9146 (ptp-110) cc_final: 0.8913 (ptp-170)
REVERT: F  278 VAL cc_start: 0.9193 (t) cc_final: 0.8136 (t)
REVERT: F  359 TYR cc_start: 0.8222 (t80) cc_final: 0.7668 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0771
  time to fit residues: 9.6103
Evaluate side-chains
  70 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 42 optimal weight:    0.6980
   chunk 63 optimal weight:    0.1980
   chunk 22 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 298 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.083298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.061182 restraints weight = 21203.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.063280 restraints weight = 12321.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.064760 restraints weight = 8677.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.065763 restraints weight = 6838.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.066168 restraints weight = 5810.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.099   5188  Z= 0.217
  Angle     :  0.664   7.425   7041  Z= 0.345
  Chirality :  0.042   0.153    810
  Planarity :  0.004   0.038    904
  Dihedral  :  5.434  44.914    724
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.92 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.33), residues: 665
  helix:  0.97 (0.47), residues: 145
  sheet: -0.56 (0.37), residues: 183
  loop : -1.23 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  72 
 TYR   0.021   0.002   TYR E  89 
 PHE   0.011   0.002   PHE F 207 
 TRP   0.020   0.002   TRP E  37 
 HIS   0.007   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 5179)
  covalent geometry    : angle       0.66281 ( 7023)
  SS BOND              : bond        0.00447 (    9)
  SS BOND              : angle       1.00536 (   18)
  hydrogen bonds       : bond        0.03644 (  192)
  hydrogen bonds       : angle       4.73626 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: D   57 TYR cc_start: 0.9013 (m-10) cc_final: 0.8776 (m-80)
REVERT: D  100 LEU cc_start: 0.8498 (tt) cc_final: 0.8264 (tt)
REVERT: E   89 TYR cc_start: 0.8811 (m-80) cc_final: 0.8461 (m-80)
REVERT: F   39 LEU cc_start: 0.9618 (mp) cc_final: 0.9239 (mp)
REVERT: F  193 PHE cc_start: 0.9279 (t80) cc_final: 0.8858 (t80)
REVERT: F  202 ASN cc_start: 0.9356 (t0) cc_final: 0.9047 (t0)
REVERT: F  205 ARG cc_start: 0.9196 (ptp-110) cc_final: 0.8946 (ptp-170)
REVERT: F  278 VAL cc_start: 0.9371 (t) cc_final: 0.8498 (t)
REVERT: F  359 TYR cc_start: 0.8263 (t80) cc_final: 0.7937 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0676
  time to fit residues: 8.1662
Evaluate side-chains
  65 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 13 optimal weight:    0.3980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 298 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.087121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.065466 restraints weight = 20873.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.067660 restraints weight = 12141.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.069238 restraints weight = 8509.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.070275 restraints weight = 6693.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.070869 restraints weight = 5679.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5188  Z= 0.113
  Angle     :  0.625   8.102   7041  Z= 0.317
  Chirality :  0.042   0.177    810
  Planarity :  0.003   0.032    904
  Dihedral  :  5.139  41.629    724
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.13 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.50 (0.33), residues: 665
  helix:  1.21 (0.48), residues: 140
  sheet: -0.16 (0.39), residues: 175
  loop : -1.07 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  76 
 TYR   0.013   0.001   TYR E  93 
 PHE   0.009   0.001   PHE F 451 
 TRP   0.039   0.002   TRP E  37 
 HIS   0.004   0.001   HIS E  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5179)
  covalent geometry    : angle       0.62426 ( 7023)
  SS BOND              : bond        0.00374 (    9)
  SS BOND              : angle       0.77709 (   18)
  hydrogen bonds       : bond        0.03059 (  192)
  hydrogen bonds       : angle       4.46774 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   47 TRP cc_start: 0.8718 (t60) cc_final: 0.7806 (t60)
REVERT: E   36 HIS cc_start: 0.7126 (m170) cc_final: 0.6549 (m90)
REVERT: E   39 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8252 (pp30)
REVERT: F   39 LEU cc_start: 0.9545 (mp) cc_final: 0.9087 (mp)
REVERT: F  193 PHE cc_start: 0.9203 (t80) cc_final: 0.8877 (t80)
REVERT: F  202 ASN cc_start: 0.9392 (t0) cc_final: 0.9067 (t0)
REVERT: F  278 VAL cc_start: 0.9218 (t) cc_final: 0.8229 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0688
  time to fit residues: 8.9920
Evaluate side-chains
  68 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0870
   chunk 59 optimal weight:   10.0000
   overall best weight:    1.3760

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 298 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.085744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.064264 restraints weight = 20656.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.066546 restraints weight = 11746.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.068055 restraints weight = 8116.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.069120 restraints weight = 6332.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.069796 restraints weight = 5357.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5188  Z= 0.140
  Angle     :  0.631   7.836   7041  Z= 0.322
  Chirality :  0.042   0.194    810
  Planarity :  0.003   0.037    904
  Dihedral  :  5.215  42.688    724
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  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: -0.52 (0.33), residues: 665
  helix:  1.24 (0.48), residues: 140
  sheet: -0.20 (0.38), residues: 176
  loop : -1.08 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  76 
 TYR   0.012   0.001   TYR E  89 
 PHE   0.010   0.001   PHE E  33 
 TRP   0.033   0.002   TRP E  37 
 HIS   0.004   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5179)
  covalent geometry    : angle       0.63056 ( 7023)
  SS BOND              : bond        0.00390 (    9)
  SS BOND              : angle       0.87686 (   18)
  hydrogen bonds       : bond        0.03318 (  192)
  hydrogen bonds       : angle       4.54969 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: D   47 TRP cc_start: 0.8719 (t60) cc_final: 0.7758 (t60)
REVERT: E   36 HIS cc_start: 0.7365 (m170) cc_final: 0.6645 (m90)
REVERT: E   38 TYR cc_start: 0.8055 (m-80) cc_final: 0.7679 (m-80)
REVERT: E   87 ASP cc_start: 0.8960 (m-30) cc_final: 0.8674 (m-30)
REVERT: E  107 LEU cc_start: 0.8672 (tp) cc_final: 0.8433 (tp)
REVERT: F   39 LEU cc_start: 0.9578 (mp) cc_final: 0.9126 (mp)
REVERT: F  193 PHE cc_start: 0.9241 (t80) cc_final: 0.8833 (t80)
REVERT: F  202 ASN cc_start: 0.9348 (t0) cc_final: 0.8988 (t0)
REVERT: F  278 VAL cc_start: 0.9263 (t) cc_final: 0.8297 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0697
  time to fit residues: 8.6165
Evaluate side-chains
  65 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 1 optimal weight:    9.9990
   chunk 6 optimal weight:    0.3980
   chunk 54 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.084837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.065037 restraints weight = 20700.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.066645 restraints weight = 9880.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.066999 restraints weight = 7414.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.067260 restraints weight = 6725.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.067595 restraints weight = 6272.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   5188  Z= 0.169
  Angle     :  0.670   7.726   7041  Z= 0.340
  Chirality :  0.042   0.186    810
  Planarity :  0.004   0.044    904
  Dihedral  :  5.375  43.090    724
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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: -0.73 (0.33), residues: 665
  helix:  0.93 (0.47), residues: 146
  sheet: -0.23 (0.39), residues: 176
  loop : -1.24 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  76 
 TYR   0.011   0.002   TYR F 359 
 PHE   0.011   0.001   PHE F  48 
 TRP   0.031   0.002   TRP E  37 
 HIS   0.005   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 5179)
  covalent geometry    : angle       0.66872 ( 7023)
  SS BOND              : bond        0.00400 (    9)
  SS BOND              : angle       0.94673 (   18)
  hydrogen bonds       : bond        0.03471 (  192)
  hydrogen bonds       : angle       4.64852 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   47 TRP cc_start: 0.8833 (t60) cc_final: 0.7835 (t60)
REVERT: D   57 TYR cc_start: 0.8838 (m-10) cc_final: 0.8583 (m-10)
REVERT: E   36 HIS cc_start: 0.7469 (m170) cc_final: 0.6859 (m90)
REVERT: E   38 TYR cc_start: 0.7961 (m-80) cc_final: 0.7535 (m-80)
REVERT: E   89 TYR cc_start: 0.8795 (m-80) cc_final: 0.8569 (m-80)
REVERT: F   39 LEU cc_start: 0.9562 (mp) cc_final: 0.9161 (mp)
REVERT: F  193 PHE cc_start: 0.9278 (t80) cc_final: 0.8848 (t80)
REVERT: F  202 ASN cc_start: 0.9391 (t0) cc_final: 0.9041 (t0)
REVERT: F  278 VAL cc_start: 0.9292 (t) cc_final: 0.8370 (t)
REVERT: F  359 TYR cc_start: 0.8247 (t80) cc_final: 0.7888 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0834
  time to fit residues: 10.0745
Evaluate side-chains
  64 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 60 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.7764

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.084453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.062725 restraints weight = 20634.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.064953 restraints weight = 11703.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.066472 restraints weight = 8124.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.067487 restraints weight = 6383.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.067878 restraints weight = 5430.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   5188  Z= 0.166
  Angle     :  0.676   8.314   7041  Z= 0.344
  Chirality :  0.043   0.180    810
  Planarity :  0.004   0.040    904
  Dihedral  :  5.422  42.880    724
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.73 (0.33), residues: 665
  helix:  0.93 (0.47), residues: 146
  sheet: -0.19 (0.39), residues: 176
  loop : -1.27 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  76 
 TYR   0.012   0.002   TYR F  23 
 PHE   0.015   0.001   PHE E 101 
 TRP   0.029   0.002   TRP E  37 
 HIS   0.005   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 5179)
  covalent geometry    : angle       0.67546 ( 7023)
  SS BOND              : bond        0.00419 (    9)
  SS BOND              : angle       0.91440 (   18)
  hydrogen bonds       : bond        0.03404 (  192)
  hydrogen bonds       : angle       4.67078 (  492)

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: D   47 TRP cc_start: 0.8817 (t60) cc_final: 0.7809 (t60)
REVERT: D  100 LEU cc_start: 0.8456 (tt) cc_final: 0.8237 (tt)
REVERT: E   36 HIS cc_start: 0.7599 (m170) cc_final: 0.6970 (m90)
REVERT: E   38 TYR cc_start: 0.8005 (m-80) cc_final: 0.7675 (m-80)
REVERT: F   39 LEU cc_start: 0.9583 (mp) cc_final: 0.9151 (mp)
REVERT: F  193 PHE cc_start: 0.9239 (t80) cc_final: 0.8822 (t80)
REVERT: F  202 ASN cc_start: 0.9340 (t0) cc_final: 0.8970 (t0)
REVERT: F  278 VAL cc_start: 0.9275 (t) cc_final: 0.8317 (t)
REVERT: F  359 TYR cc_start: 0.8063 (t80) cc_final: 0.7812 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0735
  time to fit residues: 8.8078
Evaluate side-chains
  69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.086895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.065464 restraints weight = 20564.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.067875 restraints weight = 11448.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.069413 restraints weight = 7791.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.070526 restraints weight = 6043.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.071165 restraints weight = 5083.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5188  Z= 0.113
  Angle     :  0.630   8.579   7041  Z= 0.320
  Chirality :  0.042   0.174    810
  Planarity :  0.003   0.032    904
  Dihedral  :  5.189  41.304    724
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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: -0.56 (0.33), residues: 665
  helix:  0.99 (0.47), residues: 146
  sheet:  0.02 (0.39), residues: 175
  loop : -1.19 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  87 
 TYR   0.012   0.001   TYR E  93 
 PHE   0.011   0.001   PHE F  48 
 TRP   0.027   0.002   TRP E  37 
 HIS   0.002   0.000   HIS E  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5179)
  covalent geometry    : angle       0.62924 ( 7023)
  SS BOND              : bond        0.00341 (    9)
  SS BOND              : angle       0.81239 (   18)
  hydrogen bonds       : bond        0.03155 (  192)
  hydrogen bonds       : angle       4.55082 (  492)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 959.95 seconds
wall clock time: 17 minutes 17.00 seconds (1037.00 seconds total)