Starting phenix.real_space_refine
on Tue Mar  3 13:01:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r0j_14223/03_2026/7r0j_14223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r0j_14223/03_2026/7r0j_14223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r0j_14223/03_2026/7r0j_14223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r0j_14223/03_2026/7r0j_14223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r0j_14223/03_2026/7r0j_14223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r0j_14223/03_2026/7r0j_14223.cif"
  }
  resolution = 4.23
  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=   0.019 sd=   0.045
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      19      5.16       5
     C    2947      2.51       5
     N     793      2.21       5
     O     904      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4669
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 104
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 2815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2815
          Classifications: {'peptide': 354}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 325}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1750
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220}
          Chain breaks: 1
  Time building chain proxies: 1.27, per 1000 atoms: 0.27
  Number of scatterers: 4669
  At special positions: 0
  Unit cell: (87.04, 99.84, 88.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P       6     15.00
     O     904      8.00
     N     793      7.00
     C    2947      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 103 " - pdb=" SG  CYS D 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 148 " - pdb=" SG  CYS D 222 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 347.4 milliseconds
  

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1122

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 10 sheets defined
      4.4% alpha, 42.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'C' and resid 98 through 109
    Processing helix  chain 'C' and resid 278 through 282
    Processing helix  chain 'D' and resid 188 through 191
    Processing helix  chain 'D' and resid 213 through 217
    Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 364
    Processing sheet with id=AA2, first strand: chain 'C' and resid 76 through 87
      removed outlier: 6.573A  pdb=" N   CYS C  59 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   VAL C  81 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU C  57 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ASN C  83 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL C  55 " --> pdb=" O   ASN C  83 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   GLN C  85 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   VAL C  53 " --> pdb=" O   GLN C  85 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   GLY C 141 " --> pdb=" O   ARG C  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 87
      removed outlier: 6.573A  pdb=" N   CYS C  59 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   VAL C  81 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU C  57 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ASN C  83 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL C  55 " --> pdb=" O   ASN C  83 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   GLN C  85 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   VAL C  53 " --> pdb=" O   GLN C  85 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   GLY C 141 " --> pdb=" O   ARG C  62 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 183 through 188
    Processing sheet with id=AA5, first strand: chain 'C' and resid 250 through 258
      removed outlier: 3.625A  pdb=" N   CYS C 251 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL C 235 " --> pdb=" O   VAL C 253 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   MET C 255 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ILE C 233 " --> pdb=" O   MET C 255 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   GLU C 257 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   ILE C 231 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS C 230 " --> pdb=" O   VAL C 328 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR C 321 " --> pdb=" O   PHE C 349 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 7 through 9
    Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 15
      removed outlier: 5.764A  pdb=" N   GLN D  40 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   LEU D  49 " --> pdb=" O   GLN D  40 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 13 through 15
    Processing sheet with id=AA9, first strand: chain 'D' and resid 129 through 133
    Processing sheet with id=AB1, first strand: chain 'D' and resid 136 through 138
      removed outlier: 5.925A  pdb=" N   ARG D 164 " --> pdb=" O   TRP D 173 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   TRP D 173 " --> pdb=" O   ARG D 164 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    462 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: 0.79

  Time building geometry restraints manager: 0.55 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: 1499
        1.34 -     1.46: 1124
        1.46 -     1.58: 2103
        1.58 -     1.70: 22
        1.70 -     1.82: 24
  Bond restraints: 4772
  Sorted by residual:
  bond pdb=" OG1 TPO A 360 "
       pdb=" P   TPO A 360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.602  0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" OG1 TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.616  0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" C   ASN C 122 "
       pdb=" N   LEU C 123 "
    ideal  model  delta    sigma   weight residual
    1.331  1.257  0.075 1.59e-02 3.96e+03 2.21e+01
  bond pdb=" O1P TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" O1P TPO A 360 "
       pdb=" P   TPO A 360 "
    ideal  model  delta    sigma   weight residual
    1.525  1.608 -0.083 2.00e-02 2.50e+03 1.72e+01
  ... (remaining 4767 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 6327
        2.83 -     5.67: 138
        5.67 -     8.50: 18
        8.50 -    11.34: 1
       11.34 -    14.17: 2
  Bond angle restraints: 6486
  Sorted by residual:
  angle pdb=" C   GLN D  41 "
        pdb=" N   LYS D  42 "
        pdb=" CA  LYS D  42 "
      ideal   model   delta    sigma   weight residual
     121.80  134.13  -12.33 2.44e+00 1.68e-01 2.55e+01
  angle pdb=" CB  TPO A 360 "
        pdb=" OG1 TPO A 360 "
        pdb=" P   TPO A 360 "
      ideal   model   delta    sigma   weight residual
     119.31  105.14   14.17 3.00e+00 1.11e-01 2.23e+01
  angle pdb=" N   GLY C 141 "
        pdb=" CA  GLY C 141 "
        pdb=" C   GLY C 141 "
      ideal   model   delta    sigma   weight residual
     110.74  117.04   -6.30 1.37e+00 5.33e-01 2.11e+01
  angle pdb=" N   LYS C  49 "
        pdb=" CA  LYS C  49 "
        pdb=" C   LYS C  49 "
      ideal   model   delta    sigma   weight residual
     114.31  108.80    5.51 1.29e+00 6.01e-01 1.82e+01
  angle pdb=" N   ASP C 259 "
        pdb=" CA  ASP C 259 "
        pdb=" C   ASP C 259 "
      ideal   model   delta    sigma   weight residual
     112.97  109.15    3.82 1.06e+00 8.90e-01 1.30e+01
  ... (remaining 6481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 2650
       17.88 -    35.77: 205
       35.77 -    53.65: 30
       53.65 -    71.53: 5
       71.53 -    89.41: 6
  Dihedral angle restraints: 2896
    sinusoidal: 1152
      harmonic: 1744
  Sorted by residual:
  dihedral pdb=" CB  CYS D  26 "
           pdb=" SG  CYS D  26 "
           pdb=" SG  CYS D  91 "
           pdb=" CB  CYS D  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.57   43.43     1      1.00e+01 1.00e-02 2.63e+01
  dihedral pdb=" CA  ARG D 226 "
           pdb=" C   ARG D 226 "
           pdb=" N   GLN D 227 "
           pdb=" CA  GLN D 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.12  -21.88     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  LYS C  17 "
           pdb=" C   LYS C  17 "
           pdb=" N   LEU C  18 "
           pdb=" CA  LEU C  18 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.30  -21.70     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 2893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 433
       0.035 -    0.069: 180
       0.069 -    0.103: 86
       0.103 -    0.138: 23
       0.138 -    0.172: 5
  Chirality restraints: 727
  Sorted by residual:
  chirality pdb=" CG  LEU D  76 "
            pdb=" CB  LEU D  76 "
            pdb=" CD1 LEU D  76 "
            pdb=" CD2 LEU D  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.41e-01
  chirality pdb=" CA  VAL C  81 "
            pdb=" N   VAL C  81 "
            pdb=" C   VAL C  81 "
            pdb=" CB  VAL C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  VAL C 220 "
            pdb=" N   VAL C 220 "
            pdb=" C   VAL C 220 "
            pdb=" CB  VAL C 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 724 not shown)

  Planarity restraints: 825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 236 "   -0.011 2.00e-02 2.50e+03   1.62e-02 6.56e+00
        pdb=" CG  TRP D 236 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 236 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 236 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 236 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 236 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 236 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 236 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 236 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 236 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 229 "    0.010 2.00e-02 2.50e+03   1.39e-02 4.86e+00
        pdb=" CG  TRP D 229 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 229 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 229 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 229 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 229 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 229 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 229 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 229 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 229 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 195 "   -0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO C 196 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C 196 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 196 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 822 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 123
        2.60 -     3.18: 4591
        3.18 -     3.75: 7627
        3.75 -     4.33: 10265
        4.33 -     4.90: 15822
  Nonbonded interactions: 38428
  Sorted by model distance:
  nonbonded pdb=" O   ASP D  85 "
            pdb=" OH  TYR D  89 "
     model   vdw
     2.029 3.040
  nonbonded pdb=" NE2 GLN D  92 "
            pdb=" O   GLN D  93 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" N   GLN C 130 "
            pdb=" O   LEU C 287 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" O   ALA C 263 "
            pdb=" OG  SER C 266 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   SER D 178 "
            pdb=" N   GLY D 182 "
     model   vdw
     2.193 3.120
  ... (remaining 38423 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:             0.260
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.290
  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:1.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
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      :  0.015   0.848   4776  Z= 1.288
  Angle     :  1.035  14.169   6492  Z= 0.554
  Chirality :  0.048   0.172    727
  Planarity :  0.006   0.055    825
  Dihedral  : 13.438  89.415   1765
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 37.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.00 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.99 (0.35), residues: 577
  helix: -1.30 (1.09), residues: 17
  sheet: -0.35 (0.34), residues: 245
  loop : -0.80 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 312 
 TYR   0.027   0.003   TYR D  90 
 PHE   0.023   0.003   PHE D 228 
 TRP   0.040   0.006   TRP D 236 
 HIS   0.007   0.002   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00781 ( 4772)
  covalent geometry    : angle       1.03410 ( 6486)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       1.40336 (    6)
  hydrogen bonds       : bond        0.15981 (  164)
  hydrogen bonds       : angle       9.31468 (  462)
  Misc. bond           : bond        0.84753 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 VAL cc_start: 0.8876 (t) cc_final: 0.8454 (t)
REVERT: C   34 VAL cc_start: 0.8547 (t) cc_final: 0.8173 (t)
REVERT: C   63 TYR cc_start: 0.7302 (t80) cc_final: 0.7023 (t80)
REVERT: C   69 ASP cc_start: 0.8904 (m-30) cc_final: 0.8660 (m-30)
REVERT: C  166 LEU cc_start: 0.9118 (tt) cc_final: 0.8798 (mt)
REVERT: C  255 MET cc_start: 0.7974 (tpt) cc_final: 0.7742 (tpt)
REVERT: C  272 TYR cc_start: 0.8115 (m-80) cc_final: 0.7478 (m-80)
REVERT: D   64 ARG cc_start: 0.8462 (mmt180) cc_final: 0.8195 (mmm160)
REVERT: D  101 PHE cc_start: 0.9469 (m-80) cc_final: 0.8723 (m-80)
REVERT: D  209 MET cc_start: 0.9112 (mpp) cc_final: 0.8326 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0707
  time to fit residues: 9.9200
Evaluate side-chains
  84 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 222 ASN
** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.078815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.062552 restraints weight = 20643.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.064926 restraints weight = 12799.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.066579 restraints weight = 9188.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.067748 restraints weight = 7221.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.068537 restraints weight = 6037.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
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      :  0.005   0.038   4776  Z= 0.238
  Angle     :  0.733   8.026   6492  Z= 0.373
  Chirality :  0.044   0.148    727
  Planarity :  0.005   0.036    825
  Dihedral  :  8.301  83.254    667
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 22.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.04 (0.35), residues: 577
  helix: -1.00 (1.25), residues: 17
  sheet: -0.41 (0.33), residues: 244
  loop : -0.84 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 164 
 TYR   0.017   0.002   TYR D  90 
 PHE   0.018   0.003   PHE D  74 
 TRP   0.027   0.005   TRP D 229 
 HIS   0.006   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 4772)
  covalent geometry    : angle       0.73193 ( 6486)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       1.48426 (    6)
  hydrogen bonds       : bond        0.04453 (  164)
  hydrogen bonds       : angle       7.58869 (  462)
  Misc. bond           : bond        0.00082 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7289 (t80) cc_final: 0.7083 (t80)
REVERT: C   69 ASP cc_start: 0.8515 (m-30) cc_final: 0.8305 (m-30)
REVERT: C  117 PHE cc_start: 0.8280 (m-80) cc_final: 0.8070 (m-80)
REVERT: C  272 TYR cc_start: 0.8523 (m-80) cc_final: 0.7758 (m-80)
REVERT: C  327 LEU cc_start: 0.9774 (mt) cc_final: 0.9556 (mt)
REVERT: C  352 MET cc_start: 0.8258 (ppp) cc_final: 0.8030 (ppp)
REVERT: D   64 ARG cc_start: 0.8873 (mmt180) cc_final: 0.8655 (mmm160)
REVERT: D  101 PHE cc_start: 0.9667 (m-80) cc_final: 0.9040 (m-80)
REVERT: D  162 TRP cc_start: 0.7887 (m100) cc_final: 0.7630 (m100)
REVERT: D  209 MET cc_start: 0.9364 (mpp) cc_final: 0.8743 (mpp)
REVERT: D  229 TRP cc_start: 0.8307 (m100) cc_final: 0.8075 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0565
  time to fit residues: 7.7214
Evaluate side-chains
  85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 219 HIS
C 222 ASN
C 281 ASN
C 311 ASN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.079224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.063081 restraints weight = 19678.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.065458 restraints weight = 12071.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.067106 restraints weight = 8604.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.068330 restraints weight = 6729.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.069248 restraints weight = 5570.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4776  Z= 0.196
  Angle     :  0.677   8.172   6492  Z= 0.346
  Chirality :  0.043   0.140    727
  Planarity :  0.005   0.041    825
  Dihedral  :  8.183  85.409    667
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 20.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.98 (0.35), residues: 577
  helix: -0.93 (1.23), residues: 17
  sheet: -0.44 (0.32), residues: 249
  loop : -0.72 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 164 
 TYR   0.013   0.002   TYR C 113 
 PHE   0.024   0.002   PHE D 228 
 TRP   0.014   0.003   TRP D 236 
 HIS   0.004   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 4772)
  covalent geometry    : angle       0.67660 ( 6486)
  SS BOND              : bond        0.00326 (    3)
  SS BOND              : angle       1.28278 (    6)
  hydrogen bonds       : bond        0.04232 (  164)
  hydrogen bonds       : angle       7.13732 (  462)
  Misc. bond           : bond        0.00013 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   69 ASP cc_start: 0.8494 (m-30) cc_final: 0.8292 (m-30)
REVERT: C  117 PHE cc_start: 0.8382 (m-80) cc_final: 0.8166 (m-80)
REVERT: C  130 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8408 (tm-30)
REVERT: C  272 TYR cc_start: 0.8537 (m-80) cc_final: 0.7836 (m-80)
REVERT: C  350 THR cc_start: 0.9413 (p) cc_final: 0.9206 (t)
REVERT: C  352 MET cc_start: 0.8489 (ppp) cc_final: 0.8249 (ppp)
REVERT: D   64 ARG cc_start: 0.8872 (mmt180) cc_final: 0.8651 (mmm160)
REVERT: D  101 PHE cc_start: 0.9657 (m-80) cc_final: 0.8823 (m-80)
REVERT: D  146 LEU cc_start: 0.8772 (mt) cc_final: 0.8477 (mt)
REVERT: D  209 MET cc_start: 0.9327 (mpp) cc_final: 0.8945 (mpp)
REVERT: D  216 ASP cc_start: 0.8714 (m-30) cc_final: 0.8506 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0614
  time to fit residues: 8.4000
Evaluate side-chains
  83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 19 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 47 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 46 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.075035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.060108 restraints weight = 20538.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.062267 restraints weight = 12667.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.063804 restraints weight = 9041.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.064928 restraints weight = 7067.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.065747 restraints weight = 5857.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   4776  Z= 0.316
  Angle     :  0.796   9.772   6492  Z= 0.405
  Chirality :  0.045   0.143    727
  Planarity :  0.006   0.047    825
  Dihedral  :  8.468  84.118    667
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 26.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.27 (0.35), residues: 577
  helix: -1.54 (1.07), residues: 17
  sheet: -0.66 (0.32), residues: 243
  loop : -0.87 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 145 
 TYR   0.017   0.003   TYR D  39 
 PHE   0.022   0.003   PHE D  74 
 TRP   0.017   0.004   TRP D 236 
 HIS   0.006   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00647 ( 4772)
  covalent geometry    : angle       0.79580 ( 6486)
  SS BOND              : bond        0.00648 (    3)
  SS BOND              : angle       1.01485 (    6)
  hydrogen bonds       : bond        0.04865 (  164)
  hydrogen bonds       : angle       7.79873 (  462)
  Misc. bond           : bond        0.00078 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  130 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8410 (tm-30)
REVERT: C  272 TYR cc_start: 0.8527 (m-80) cc_final: 0.7825 (m-80)
REVERT: C  327 LEU cc_start: 0.9771 (mt) cc_final: 0.9516 (mt)
REVERT: C  352 MET cc_start: 0.8574 (ppp) cc_final: 0.8342 (ppp)
REVERT: D  101 PHE cc_start: 0.9643 (m-80) cc_final: 0.9293 (m-80)
REVERT: D  146 LEU cc_start: 0.8831 (mt) cc_final: 0.8546 (mt)
REVERT: D  209 MET cc_start: 0.9109 (mpp) cc_final: 0.8631 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0658
  time to fit residues: 8.3563
Evaluate side-chains
  76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

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 = 0.079649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.063447 restraints weight = 19529.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.065844 restraints weight = 12033.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.067499 restraints weight = 8580.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.068721 restraints weight = 6687.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.069613 restraints weight = 5533.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4776  Z= 0.153
  Angle     :  0.662   8.578   6492  Z= 0.333
  Chirality :  0.043   0.140    727
  Planarity :  0.005   0.047    825
  Dihedral  :  8.157  86.072    667
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 17.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.18 (0.35), residues: 577
  helix: -0.86 (1.17), residues: 17
  sheet: -0.71 (0.32), residues: 250
  loop : -0.74 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  65 
 TYR   0.010   0.002   TYR C 113 
 PHE   0.011   0.002   PHE D 101 
 TRP   0.024   0.004   TRP D 236 
 HIS   0.002   0.001   HIS D 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4772)
  covalent geometry    : angle       0.66097 ( 6486)
  SS BOND              : bond        0.00291 (    3)
  SS BOND              : angle       1.13765 (    6)
  hydrogen bonds       : bond        0.03841 (  164)
  hydrogen bonds       : angle       6.89821 (  462)
  Misc. bond           : bond        0.00000 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.8041 (t80) cc_final: 0.7782 (t80)
REVERT: C   69 ASP cc_start: 0.8408 (m-30) cc_final: 0.8196 (m-30)
REVERT: C  117 PHE cc_start: 0.8249 (m-80) cc_final: 0.7663 (m-80)
REVERT: C  130 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8433 (tm-30)
REVERT: C  272 TYR cc_start: 0.8649 (m-80) cc_final: 0.7938 (m-80)
REVERT: C  311 ASN cc_start: 0.7263 (t0) cc_final: 0.7003 (t0)
REVERT: C  350 THR cc_start: 0.9437 (p) cc_final: 0.9231 (t)
REVERT: D   74 PHE cc_start: 0.8147 (m-80) cc_final: 0.7920 (m-80)
REVERT: D  101 PHE cc_start: 0.9616 (m-80) cc_final: 0.8661 (m-80)
REVERT: D  146 LEU cc_start: 0.8873 (mt) cc_final: 0.8610 (mt)
REVERT: D  209 MET cc_start: 0.9225 (mpp) cc_final: 0.8970 (mpp)
REVERT: D  216 ASP cc_start: 0.8739 (m-30) cc_final: 0.8500 (m-30)
REVERT: D  229 TRP cc_start: 0.8479 (m100) cc_final: 0.7921 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0650
  time to fit residues: 8.3493
Evaluate side-chains
  83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.078310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.062223 restraints weight = 20054.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.064611 restraints weight = 12117.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.066306 restraints weight = 8529.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.067446 restraints weight = 6596.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.068387 restraints weight = 5469.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4776  Z= 0.197
  Angle     :  0.676   8.438   6492  Z= 0.342
  Chirality :  0.043   0.143    727
  Planarity :  0.005   0.046    825
  Dihedral  :  8.145  84.738    667
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 19.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.09 (0.35), residues: 577
  helix: -0.73 (1.22), residues: 17
  sheet: -0.61 (0.32), residues: 250
  loop : -0.72 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  65 
 TYR   0.015   0.002   TYR D 183 
 PHE   0.032   0.002   PHE D 228 
 TRP   0.018   0.004   TRP D 236 
 HIS   0.004   0.001   HIS C 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4772)
  covalent geometry    : angle       0.67541 ( 6486)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       0.95701 (    6)
  hydrogen bonds       : bond        0.03946 (  164)
  hydrogen bonds       : angle       6.99682 (  462)
  Misc. bond           : bond        0.00016 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7952 (t80) cc_final: 0.7647 (t80)
REVERT: C  117 PHE cc_start: 0.8310 (m-80) cc_final: 0.7761 (m-80)
REVERT: C  130 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8415 (tm-30)
REVERT: C  166 LEU cc_start: 0.8809 (tt) cc_final: 0.8517 (mp)
REVERT: C  272 TYR cc_start: 0.8618 (m-80) cc_final: 0.7922 (m-80)
REVERT: C  311 ASN cc_start: 0.7124 (t0) cc_final: 0.6838 (t0)
REVERT: C  350 THR cc_start: 0.9439 (p) cc_final: 0.9234 (t)
REVERT: D  101 PHE cc_start: 0.9606 (m-80) cc_final: 0.8614 (m-80)
REVERT: D  146 LEU cc_start: 0.8842 (mt) cc_final: 0.8567 (mt)
REVERT: D  209 MET cc_start: 0.9208 (mpp) cc_final: 0.8871 (mpp)
REVERT: D  216 ASP cc_start: 0.8725 (m-30) cc_final: 0.8512 (m-30)
REVERT: D  229 TRP cc_start: 0.8138 (m100) cc_final: 0.7744 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0570
  time to fit residues: 7.3622
Evaluate side-chains
  78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0670
   chunk 20 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0020
   chunk 12 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.4926

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.084248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.067702 restraints weight = 19207.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.070146 restraints weight = 12008.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071874 restraints weight = 8576.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.073098 restraints weight = 6678.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.074056 restraints weight = 5539.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4776  Z= 0.119
  Angle     :  0.651   8.196   6492  Z= 0.324
  Chirality :  0.043   0.139    727
  Planarity :  0.004   0.048    825
  Dihedral  :  7.940  87.673    667
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.81 (0.35), residues: 577
  helix: -0.47 (1.31), residues: 17
  sheet: -0.36 (0.32), residues: 248
  loop : -0.60 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  65 
 TYR   0.009   0.001   TYR C 113 
 PHE   0.013   0.001   PHE D 101 
 TRP   0.024   0.004   TRP D  38 
 HIS   0.003   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4772)
  covalent geometry    : angle       0.64900 ( 6486)
  SS BOND              : bond        0.00743 (    3)
  SS BOND              : angle       1.82853 (    6)
  hydrogen bonds       : bond        0.03679 (  164)
  hydrogen bonds       : angle       6.30905 (  462)
  Misc. bond           : bond        0.00021 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7649 (t80) cc_final: 0.7259 (t80)
REVERT: C  117 PHE cc_start: 0.8269 (m-80) cc_final: 0.7866 (m-80)
REVERT: C  272 TYR cc_start: 0.8585 (m-80) cc_final: 0.7875 (m-80)
REVERT: C  311 ASN cc_start: 0.6939 (t0) cc_final: 0.6661 (t0)
REVERT: C  350 THR cc_start: 0.9446 (p) cc_final: 0.9245 (t)
REVERT: D  101 PHE cc_start: 0.9598 (m-80) cc_final: 0.8565 (m-80)
REVERT: D  146 LEU cc_start: 0.8804 (mt) cc_final: 0.8332 (mt)
REVERT: D  156 TYR cc_start: 0.8574 (m-10) cc_final: 0.8197 (m-10)
REVERT: D  161 HIS cc_start: 0.9420 (m-70) cc_final: 0.9029 (m90)
REVERT: D  209 MET cc_start: 0.9113 (mpp) cc_final: 0.8579 (mpp)
REVERT: D  216 ASP cc_start: 0.8626 (m-30) cc_final: 0.8284 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0595
  time to fit residues: 8.4121
Evaluate side-chains
  86 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0020
   chunk 13 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   overall best weight:    0.8190

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 ASN
D 227 GLN
D 238 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.084486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.067918 restraints weight = 19217.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.070348 restraints weight = 11819.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.072141 restraints weight = 8384.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073470 restraints weight = 6481.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.074390 restraints weight = 5314.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4776  Z= 0.118
  Angle     :  0.653   7.860   6492  Z= 0.325
  Chirality :  0.043   0.140    727
  Planarity :  0.004   0.044    825
  Dihedral  :  7.760  86.368    667
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.47 (0.35), residues: 577
  helix: -0.07 (1.38), residues: 17
  sheet: -0.01 (0.33), residues: 249
  loop : -0.50 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  65 
 TYR   0.016   0.001   TYR D 183 
 PHE   0.012   0.001   PHE D 101 
 TRP   0.024   0.004   TRP D 236 
 HIS   0.006   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4772)
  covalent geometry    : angle       0.65127 ( 6486)
  SS BOND              : bond        0.00496 (    3)
  SS BOND              : angle       1.57391 (    6)
  hydrogen bonds       : bond        0.03571 (  164)
  hydrogen bonds       : angle       6.11919 (  462)
  Misc. bond           : bond        0.00022 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7483 (t80) cc_final: 0.7016 (t80)
REVERT: C  272 TYR cc_start: 0.8504 (m-80) cc_final: 0.7857 (m-80)
REVERT: C  311 ASN cc_start: 0.7124 (t0) cc_final: 0.6868 (t0)
REVERT: C  327 LEU cc_start: 0.9769 (mt) cc_final: 0.9523 (mt)
REVERT: D   86 PHE cc_start: 0.8239 (m-80) cc_final: 0.7556 (m-80)
REVERT: D  101 PHE cc_start: 0.9623 (m-80) cc_final: 0.9081 (m-80)
REVERT: D  146 LEU cc_start: 0.8745 (mt) cc_final: 0.8282 (mt)
REVERT: D  156 TYR cc_start: 0.8571 (m-10) cc_final: 0.8181 (m-10)
REVERT: D  161 HIS cc_start: 0.9420 (m-70) cc_final: 0.9178 (m90)
REVERT: D  209 MET cc_start: 0.9097 (mpp) cc_final: 0.8588 (mpp)
REVERT: D  216 ASP cc_start: 0.8621 (m-30) cc_final: 0.8374 (m-30)
REVERT: D  229 TRP cc_start: 0.8461 (m100) cc_final: 0.8033 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0587
  time to fit residues: 8.2591
Evaluate side-chains
  83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0370
   chunk 44 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    3.3864

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

Flipped N/Q/H residues before XYZ refinement:
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 GLN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
D 227 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.080773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.064804 restraints weight = 19743.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.067087 restraints weight = 12141.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.068741 restraints weight = 8674.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.069770 restraints weight = 6760.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.070756 restraints weight = 5686.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4776  Z= 0.188
  Angle     :  0.683   6.766   6492  Z= 0.348
  Chirality :  0.043   0.147    727
  Planarity :  0.005   0.044    825
  Dihedral  :  7.879  84.005    667
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.18 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.69 (0.35), residues: 577
  helix: -0.10 (1.33), residues: 17
  sheet: -0.13 (0.33), residues: 234
  loop : -0.67 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  65 
 TYR   0.011   0.002   TYR C 173 
 PHE   0.019   0.002   PHE D  74 
 TRP   0.026   0.004   TRP D 236 
 HIS   0.005   0.001   HIS C 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 4772)
  covalent geometry    : angle       0.68216 ( 6486)
  SS BOND              : bond        0.00299 (    3)
  SS BOND              : angle       1.24434 (    6)
  hydrogen bonds       : bond        0.03970 (  164)
  hydrogen bonds       : angle       6.57789 (  462)
  Misc. bond           : bond        0.00015 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7562 (t80) cc_final: 0.7250 (t80)
REVERT: C  272 TYR cc_start: 0.8484 (m-80) cc_final: 0.7944 (m-80)
REVERT: C  280 ASN cc_start: 0.9155 (p0) cc_final: 0.8911 (p0)
REVERT: C  311 ASN cc_start: 0.7186 (t0) cc_final: 0.6936 (t0)
REVERT: C  327 LEU cc_start: 0.9780 (mt) cc_final: 0.9544 (mt)
REVERT: D   86 PHE cc_start: 0.8487 (m-80) cc_final: 0.7732 (m-80)
REVERT: D  101 PHE cc_start: 0.9601 (m-80) cc_final: 0.9004 (m-80)
REVERT: D  146 LEU cc_start: 0.8760 (mt) cc_final: 0.8363 (mt)
REVERT: D  209 MET cc_start: 0.9177 (mpp) cc_final: 0.8691 (mpp)
REVERT: D  216 ASP cc_start: 0.8686 (m-30) cc_final: 0.8450 (m-30)
REVERT: D  229 TRP cc_start: 0.8400 (m100) cc_final: 0.8004 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0655
  time to fit residues: 8.7178
Evaluate side-chains
  81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 1 optimal weight:    0.4980
   chunk 40 optimal weight:    0.0470
   chunk 42 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    3.7084

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.079816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.063516 restraints weight = 19627.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.065919 restraints weight = 11909.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.067643 restraints weight = 8413.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.068903 restraints weight = 6501.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.069751 restraints weight = 5341.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4776  Z= 0.203
  Angle     :  0.705   6.863   6492  Z= 0.361
  Chirality :  0.043   0.148    727
  Planarity :  0.005   0.043    825
  Dihedral  :  8.051  84.391    667
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 19.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.71 (0.35), residues: 577
  helix: -0.29 (1.32), residues: 17
  sheet: -0.22 (0.33), residues: 240
  loop : -0.61 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 145 
 TYR   0.018   0.002   TYR C  21 
 PHE   0.018   0.002   PHE D  74 
 TRP   0.028   0.005   TRP D 229 
 HIS   0.010   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4772)
  covalent geometry    : angle       0.70479 ( 6486)
  SS BOND              : bond        0.00320 (    3)
  SS BOND              : angle       1.24078 (    6)
  hydrogen bonds       : bond        0.04024 (  164)
  hydrogen bonds       : angle       6.78400 (  462)
  Misc. bond           : bond        0.00004 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7752 (t80) cc_final: 0.7429 (t80)
REVERT: C  117 PHE cc_start: 0.8111 (m-10) cc_final: 0.7894 (m-10)
REVERT: C  272 TYR cc_start: 0.8531 (m-80) cc_final: 0.7981 (m-80)
REVERT: D   74 PHE cc_start: 0.8189 (m-80) cc_final: 0.7981 (m-80)
REVERT: D   86 PHE cc_start: 0.8502 (m-80) cc_final: 0.7676 (m-80)
REVERT: D  101 PHE cc_start: 0.9612 (m-80) cc_final: 0.9012 (m-80)
REVERT: D  146 LEU cc_start: 0.8765 (mt) cc_final: 0.8454 (mt)
REVERT: D  209 MET cc_start: 0.9226 (mpp) cc_final: 0.8893 (mpp)
REVERT: D  216 ASP cc_start: 0.8811 (m-30) cc_final: 0.8586 (m-30)
REVERT: D  229 TRP cc_start: 0.8353 (m100) cc_final: 0.7822 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0684
  time to fit residues: 8.7604
Evaluate side-chains
  78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 54 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 295 HIS
D  40 GLN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 208 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.075464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.059840 restraints weight = 20236.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.062124 restraints weight = 12356.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.063751 restraints weight = 8730.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.064952 restraints weight = 6776.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.065659 restraints weight = 5604.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   4776  Z= 0.306
  Angle     :  0.811   8.262   6492  Z= 0.416
  Chirality :  0.046   0.156    727
  Planarity :  0.005   0.043    825
  Dihedral  :  8.514  85.173    667
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 27.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.59 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -1.17 (0.35), residues: 577
  helix: -2.02 (0.88), residues: 23
  sheet: -0.54 (0.33), residues: 237
  loop : -0.78 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 363 
 TYR   0.020   0.003   TYR D 183 
 PHE   0.024   0.003   PHE D  74 
 TRP   0.033   0.006   TRP D 236 
 HIS   0.008   0.002   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 ( 4772)
  covalent geometry    : angle       0.81006 ( 6486)
  SS BOND              : bond        0.00140 (    3)
  SS BOND              : angle       1.35566 (    6)
  hydrogen bonds       : bond        0.04816 (  164)
  hydrogen bonds       : angle       7.63668 (  462)
  Misc. bond           : bond        0.00058 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 850.53 seconds
wall clock time: 15 minutes 29.95 seconds (929.95 seconds total)