Starting phenix.real_space_refine
on Wed Sep 17 05:51:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vu5_43526/09_2025/8vu5_43526.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vu5_43526/09_2025/8vu5_43526.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vu5_43526/09_2025/8vu5_43526.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vu5_43526/09_2025/8vu5_43526.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vu5_43526/09_2025/8vu5_43526.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vu5_43526/09_2025/8vu5_43526.map"
  }
  resolution = 3.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.018
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      31      5.16       5
     C    3583      2.51       5
     N     968      2.21       5
     O    1034      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5616
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1119
          Classifications: {'peptide': 148}
          Link IDs: {'PTRANS': 9, 'TRANS': 138}
    Chain: "B"
      Number of atoms: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2234
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 22, 'TRANS': 260}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 20
    Chain: "C"
      Number of atoms: 2263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2263
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 23, 'TRANS': 264}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 1.45, per 1000 atoms: 0.26
  Number of scatterers: 5616
  At special positions: 0
  Unit cell: (74.529, 107.289, 93.366, 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      31     16.00
     O    1034      8.00
     N     968      7.00
     C    3583      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  40 " - pdb=" SG  CYS B  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  77 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 193 " - pdb=" SG  CYS B 315 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 194 " - pdb=" SG  CYS B 233 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  40 " - pdb=" SG  CYS C  50 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  77 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 193 " - pdb=" SG  CYS C 315 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 194 " - pdb=" SG  CYS C 233 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 326 " - pdb=" SG  CYS C 343 " 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: 0.47
  Conformation dependent library (CDL) restraints added in 212.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1338

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 12 sheets defined
      17.4% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 50
      removed outlier: 3.570A  pdb=" N   LEU A  33 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER A  48 " --> pdb=" O   HIS A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 73
      removed outlier: 3.681A  pdb=" N   TRP A  72 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LYS A  73 " --> pdb=" O   GLY A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 102
    Processing helix  chain 'A' and resid 105 through 130
      removed outlier: 3.508A  pdb=" N   LEU A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 128 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 156
      removed outlier: 3.555A  pdb=" N   LEU A 148 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 167
    Processing helix  chain 'A' and resid 167 through 173
      removed outlier: 3.839A  pdb=" N   VAL A 173 " --> pdb=" O   PRO A 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 130
      No H-bonds generated for 'chain 'B' and resid 128 through 130'
    Processing helix  chain 'C' and resid 127 through 131
    Processing helix  chain 'C' and resid 275 through 280
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62
    Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41
    Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 69
    Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 187
      removed outlier: 3.599A  pdb=" N   GLN B 186 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU B 169 " --> pdb=" O   GLN B 186 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL B 268 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 359
    Processing sheet with id=AA6, first strand: chain 'C' and resid 40 through 41
      removed outlier: 3.723A  pdb=" N   CYS C  50 " --> pdb=" O   CYS C  93 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 75 through 76
      removed outlier: 3.627A  pdb=" N   HIS C 108 " --> pdb=" O   ALA C  68 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG C 123 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 154
      removed outlier: 3.641A  pdb=" N   VAL C 235 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE C 152 " --> pdb=" O   CYS C 233 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   CYS C 233 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 165 through 167
    Processing sheet with id=AB1, first strand: chain 'C' and resid 245 through 246
    Processing sheet with id=AB2, first strand: chain 'C' and resid 302 through 304
    Processing sheet with id=AB3, first strand: chain 'C' and resid 308 through 310
      removed outlier: 3.865A  pdb=" N   ARG C 308 " --> pdb=" O   HIS C 354 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   HIS C 354 " --> pdb=" O   ARG C 308 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   SER C 310 " --> pdb=" O   VAL C 352 " (cutoff:3.500A)

    137 hydrogen bonds defined for protein.
    357 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.68

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1473
        1.33 -     1.46: 1536
        1.46 -     1.59: 2721
        1.59 -     1.72: 0
        1.72 -     1.84: 35
  Bond restraints: 5765
  Sorted by residual:
  bond pdb=" CA  SER A 108 "
       pdb=" CB  SER A 108 "
    ideal  model  delta    sigma   weight residual
    1.532  1.475  0.057 1.62e-02 3.81e+03 1.24e+01
  bond pdb=" N   VAL A  65 "
       pdb=" CA  VAL A  65 "
    ideal  model  delta    sigma   weight residual
    1.458  1.506 -0.048 1.37e-02 5.33e+03 1.22e+01
  bond pdb=" N   LEU A 107 "
       pdb=" CA  LEU A 107 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.041 1.31e-02 5.83e+03 9.90e+00
  bond pdb=" C   ASP B  27 "
       pdb=" N   VAL B  28 "
    ideal  model  delta    sigma   weight residual
    1.335  1.302  0.033 1.10e-02 8.26e+03 9.10e+00
  bond pdb=" N   PHE B  41 "
       pdb=" CA  PHE B  41 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.18e-02 7.18e+03 8.60e+00
  ... (remaining 5760 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 7580
        2.00 -     4.00: 221
        4.00 -     6.00: 42
        6.00 -     8.00: 9
        8.00 -     9.99: 1
  Bond angle restraints: 7853
  Sorted by residual:
  angle pdb=" N   VAL B  28 "
        pdb=" CA  VAL B  28 "
        pdb=" CB  VAL B  28 "
      ideal   model   delta    sigma   weight residual
     110.78  100.79    9.99 1.98e+00 2.55e-01 2.55e+01
  angle pdb=" CA  VAL C 101 "
        pdb=" C   VAL C 101 "
        pdb=" O   VAL C 101 "
      ideal   model   delta    sigma   weight residual
     121.59  116.46    5.13 1.03e+00 9.43e-01 2.48e+01
  angle pdb=" N   PRO B 133 "
        pdb=" CA  PRO B 133 "
        pdb=" C   PRO B 133 "
      ideal   model   delta    sigma   weight residual
     111.15  118.88   -7.73 1.58e+00 4.01e-01 2.39e+01
  angle pdb=" N   SER A 108 "
        pdb=" CA  SER A 108 "
        pdb=" C   SER A 108 "
      ideal   model   delta    sigma   weight residual
     112.04  105.08    6.96 1.44e+00 4.82e-01 2.34e+01
  angle pdb=" C   ASP A  66 "
        pdb=" N   PHE A  67 "
        pdb=" CA  PHE A  67 "
      ideal   model   delta    sigma   weight residual
     123.05  116.57    6.48 1.40e+00 5.10e-01 2.14e+01
  ... (remaining 7848 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 2915
       17.94 -    35.87: 382
       35.87 -    53.81: 123
       53.81 -    71.75: 22
       71.75 -    89.68: 8
  Dihedral angle restraints: 3450
    sinusoidal: 1390
      harmonic: 2060
  Sorted by residual:
  dihedral pdb=" CB  CYS B 326 "
           pdb=" SG  CYS B 326 "
           pdb=" SG  CYS B 343 "
           pdb=" CB  CYS B 343 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.85   79.85     1      1.00e+01 1.00e-02 7.91e+01
  dihedral pdb=" CB  CYS A  50 "
           pdb=" SG  CYS A  50 "
           pdb=" SG  CYS A 106 "
           pdb=" CB  CYS A 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.47  -72.47     1      1.00e+01 1.00e-02 6.71e+01
  dihedral pdb=" CB  CYS C 326 "
           pdb=" SG  CYS C 326 "
           pdb=" SG  CYS C 343 "
           pdb=" CB  CYS C 343 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -20.83  -65.17     1      1.00e+01 1.00e-02 5.57e+01
  ... (remaining 3447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 757
       0.067 -    0.134: 100
       0.134 -    0.200: 11
       0.200 -    0.267: 2
       0.267 -    0.334: 1
  Chirality restraints: 871
  Sorted by residual:
  chirality pdb=" CA  VAL B  28 "
            pdb=" N   VAL B  28 "
            pdb=" C   VAL B  28 "
            pdb=" CB  VAL B  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.77   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CA  PRO B 133 "
            pdb=" N   PRO B 133 "
            pdb=" C   PRO B 133 "
            pdb=" CB  PRO B 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  VAL A  65 "
            pdb=" N   VAL A  65 "
            pdb=" C   VAL A  65 "
            pdb=" CB  VAL A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 868 not shown)

  Planarity restraints: 1011
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 102 "   -0.012 2.00e-02 2.50e+03   2.61e-02 6.82e+00
        pdb=" C   ARG C 102 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ARG C 102 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU C 103 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 156 "   -0.038 5.00e-02 4.00e+02   5.80e-02 5.38e+00
        pdb=" N   PRO C 157 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C 157 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 157 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  64 "    0.012 2.00e-02 2.50e+03   2.25e-02 5.04e+00
        pdb=" C   ALA A  64 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A  64 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A  65 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1008 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 467
        2.74 -     3.28: 5516
        3.28 -     3.82: 9270
        3.82 -     4.36: 10354
        4.36 -     4.90: 17653
  Nonbonded interactions: 43260
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  44 "
            pdb=" OD2 ASP C  47 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" N   PHE C 104 "
            pdb=" OD2 ASP C 128 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   ASP C 128 "
            pdb=" N   ARG C 258 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" N   GLU A 167 "
            pdb=" OE1 GLU A 167 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" OE1 GLU C 168 "
            pdb=" NH2 ARG C 249 "
     model   vdw
     2.355 3.120
  ... (remaining 43255 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 28 through 276 or resid 291 through 292 or resid 295 throu \ 
gh 319 or (resid 320 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 321 through 326 or resid 341 through 375))
  selection = (chain 'C' and (resid 28 through 31 or resid 36 through 53 or resid 64 through 2 \ 
78 or resid 295 through 308 or (resid 309 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 310 through 321 or (resid 322 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 323 through 375))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.000
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
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      :  0.005   0.057   5776  Z= 0.310
  Angle     :  0.811   9.994   7875  Z= 0.479
  Chirality :  0.048   0.334    871
  Planarity :  0.005   0.058   1011
  Dihedral  : 17.684  89.682   2079
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 31.14 %
    Favored  : 67.42 %
  Cbeta Deviations :  0.15 %
  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 aren not related in a simple way.
  whole: -1.20 (0.34), residues: 695
  helix:  1.67 (0.54), residues: 107
  sheet: -1.16 (0.47), residues: 146
  loop : -1.34 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 166 
 TYR   0.021   0.002   TYR C  80 
 PHE   0.021   0.002   PHE C 306 
 TRP   0.024   0.002   TRP C 110 
 HIS   0.003   0.001   HIS C 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 5765)
  covalent geometry    : angle       0.80745 ( 7853)
  SS BOND              : bond        0.00563 (   11)
  SS BOND              : angle       1.61461 (   22)
  hydrogen bonds       : bond        0.24975 (  137)
  hydrogen bonds       : angle       9.62010 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.7506 (p0) cc_final: 0.6231 (p0)
REVERT: B   98 GLN cc_start: 0.7926 (tp-100) cc_final: 0.7721 (tp40)
REVERT: B  198 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.4868 (t60)
  outliers start: 9
  outliers final: 5
  residues processed: 85
  average time/residue: 0.0754
  time to fit residues: 8.6312
Evaluate side-chains
  78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  198 TRP
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** 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 = 0.4485 r_free = 0.4485 target = 0.207034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.164826 restraints weight = 7542.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 3.45
r_work: 0.3717 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5776  Z= 0.165
  Angle     :  0.666   8.278   7875  Z= 0.336
  Chirality :  0.042   0.149    871
  Planarity :  0.005   0.059   1011
  Dihedral  :  6.434  59.217    771
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 26.48 %
    Favored  : 68.70 %
  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 aren not related in a simple way.
  whole: -1.18 (0.34), residues: 695
  helix:  1.39 (0.50), residues: 117
  sheet: -1.06 (0.43), residues: 169
  loop : -1.33 (0.33), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 166 
 TYR   0.015   0.002   TYR C  69 
 PHE   0.021   0.002   PHE B  41 
 TRP   0.016   0.002   TRP C 110 
 HIS   0.002   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5765)
  covalent geometry    : angle       0.66068 ( 7853)
  SS BOND              : bond        0.00516 (   11)
  SS BOND              : angle       1.67448 (   22)
  hydrogen bonds       : bond        0.05023 (  137)
  hydrogen bonds       : angle       6.79844 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 76
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.6904 (p0) cc_final: 0.6460 (p0)
REVERT: A   78 GLN cc_start: 0.7112 (mp10) cc_final: 0.6862 (mp10)
REVERT: B   26 GLN cc_start: 0.6297 (mt0) cc_final: 0.5970 (mm-40)
REVERT: C  105 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6974 (m-80)
REVERT: C  142 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7717 (mmt180)
  outliers start: 30
  outliers final: 12
  residues processed: 101
  average time/residue: 0.0776
  time to fit residues: 10.4126
Evaluate side-chains
  83 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain C residue   93 CYS
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  142 ARG
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  353 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 55 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 25 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN
C 151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.208201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.166381 restraints weight = 7471.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 3.45
r_work: 0.3731 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5776  Z= 0.136
  Angle     :  0.609   5.875   7875  Z= 0.305
  Chirality :  0.041   0.149    871
  Planarity :  0.005   0.058   1011
  Dihedral  :  5.699  56.579    766
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 26.48 %
    Favored  : 68.86 %
  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 aren not related in a simple way.
  whole: -1.08 (0.34), residues: 695
  helix:  1.66 (0.49), residues: 117
  sheet: -1.14 (0.42), residues: 171
  loop : -1.25 (0.33), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.010   0.001   TYR C  69 
 PHE   0.018   0.002   PHE C 105 
 TRP   0.020   0.002   TRP B 198 
 HIS   0.002   0.000   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5765)
  covalent geometry    : angle       0.60451 ( 7853)
  SS BOND              : bond        0.00395 (   11)
  SS BOND              : angle       1.51018 (   22)
  hydrogen bonds       : bond        0.04202 (  137)
  hydrogen bonds       : angle       6.23599 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.7120 (p0) cc_final: 0.6484 (p0)
REVERT: A   78 GLN cc_start: 0.7148 (mp10) cc_final: 0.6924 (mp10)
REVERT: B   26 GLN cc_start: 0.6297 (mt0) cc_final: 0.6027 (mm-40)
REVERT: B  149 GLU cc_start: 0.7133 (tp30) cc_final: 0.6812 (mm-30)
REVERT: B  257 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6552 (mm)
REVERT: C  105 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.6760 (m-80)
REVERT: C  110 TRP cc_start: 0.6958 (p-90) cc_final: 0.6654 (p-90)
  outliers start: 29
  outliers final: 16
  residues processed: 103
  average time/residue: 0.0881
  time to fit residues: 11.6388
Evaluate side-chains
  90 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue   93 CYS
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  353 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 31 optimal weight:    0.2980
   chunk 48 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** 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 = 0.4491 r_free = 0.4491 target = 0.207597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.165540 restraints weight = 7496.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.4058 rms_B_bonded: 3.40
r_work: 0.3716 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5776  Z= 0.145
  Angle     :  0.634   6.921   7875  Z= 0.316
  Chirality :  0.041   0.137    871
  Planarity :  0.005   0.058   1011
  Dihedral  :  5.625  53.423    766
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 26.48 %
    Favored  : 67.74 %
  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 aren not related in a simple way.
  whole: -1.12 (0.34), residues: 695
  helix:  1.86 (0.50), residues: 117
  sheet: -1.30 (0.42), residues: 161
  loop : -1.31 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.018   0.002   TYR C  80 
 PHE   0.021   0.002   PHE C 105 
 TRP   0.019   0.002   TRP B 198 
 HIS   0.001   0.000   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5765)
  covalent geometry    : angle       0.62096 ( 7853)
  SS BOND              : bond        0.00535 (   11)
  SS BOND              : angle       2.54084 (   22)
  hydrogen bonds       : bond        0.03937 (  137)
  hydrogen bonds       : angle       6.08395 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 77
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.7399 (p0) cc_final: 0.6607 (p0)
REVERT: A   78 GLN cc_start: 0.7203 (mp10) cc_final: 0.6837 (mp10)
REVERT: B   26 GLN cc_start: 0.6269 (mt0) cc_final: 0.6034 (mm-40)
REVERT: B  109 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6166 (mt)
REVERT: B  257 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6508 (mm)
REVERT: C  105 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6835 (m-80)
REVERT: C  110 TRP cc_start: 0.6999 (p-90) cc_final: 0.6759 (p-90)
  outliers start: 36
  outliers final: 19
  residues processed: 108
  average time/residue: 0.0798
  time to fit residues: 11.3351
Evaluate side-chains
  92 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue   93 CYS
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  353 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** 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 = 0.4478 r_free = 0.4478 target = 0.206621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.164311 restraints weight = 7589.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 3.54
r_work: 0.3694 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100   5776  Z= 0.169
  Angle     :  0.678  11.178   7875  Z= 0.336
  Chirality :  0.043   0.158    871
  Planarity :  0.005   0.058   1011
  Dihedral  :  5.883  54.631    766
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 26.81 %
    Favored  : 67.26 %
  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 aren not related in a simple way.
  whole: -1.16 (0.34), residues: 695
  helix:  1.83 (0.51), residues: 117
  sheet: -1.37 (0.41), residues: 166
  loop : -1.31 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 249 
 TYR   0.012   0.001   TYR C  69 
 PHE   0.024   0.002   PHE C 105 
 TRP   0.016   0.002   TRP B 198 
 HIS   0.001   0.000   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 5765)
  covalent geometry    : angle       0.65469 ( 7853)
  SS BOND              : bond        0.00926 (   11)
  SS BOND              : angle       3.39675 (   22)
  hydrogen bonds       : bond        0.03888 (  137)
  hydrogen bonds       : angle       6.10126 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 72
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.7646 (p0) cc_final: 0.6761 (p0)
REVERT: A   78 GLN cc_start: 0.7189 (mp10) cc_final: 0.6951 (mp10)
REVERT: B   26 GLN cc_start: 0.6442 (mt0) cc_final: 0.6180 (mm-40)
REVERT: B   46 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7117 (tm-30)
REVERT: B  149 GLU cc_start: 0.7123 (tp30) cc_final: 0.6822 (mm-30)
REVERT: B  257 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6582 (mm)
REVERT: C  105 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6824 (m-80)
REVERT: C  110 TRP cc_start: 0.7021 (p-90) cc_final: 0.6695 (p-90)
  outliers start: 37
  outliers final: 24
  residues processed: 105
  average time/residue: 0.0815
  time to fit residues: 11.1588
Evaluate side-chains
  96 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  323 TRP
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   93 CYS
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain C residue  367 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0030
   chunk 9 optimal weight:    0.6980
   chunk 43 optimal weight:    0.2980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** 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 = 0.4490 r_free = 0.4490 target = 0.208065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.166698 restraints weight = 7489.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 3.46
r_work: 0.3731 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   5776  Z= 0.135
  Angle     :  0.624  11.335   7875  Z= 0.311
  Chirality :  0.042   0.144    871
  Planarity :  0.005   0.057   1011
  Dihedral  :  5.724  55.245    766
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.09 %
    Favored  : 67.42 %
  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 aren not related in a simple way.
  whole: -1.02 (0.34), residues: 695
  helix:  2.09 (0.52), residues: 117
  sheet: -1.32 (0.42), residues: 161
  loop : -1.25 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 249 
 TYR   0.020   0.001   TYR C  80 
 PHE   0.021   0.001   PHE C 105 
 TRP   0.014   0.001   TRP B 198 
 HIS   0.001   0.000   HIS C 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5765)
  covalent geometry    : angle       0.61243 ( 7853)
  SS BOND              : bond        0.00660 (   11)
  SS BOND              : angle       2.37523 (   22)
  hydrogen bonds       : bond        0.03481 (  137)
  hydrogen bonds       : angle       5.86436 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.7524 (p0) cc_final: 0.6604 (p0)
REVERT: A   78 GLN cc_start: 0.7159 (mp10) cc_final: 0.6914 (mp10)
REVERT: B   26 GLN cc_start: 0.6401 (mt0) cc_final: 0.6082 (mm-40)
REVERT: B   46 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7087 (tm-30)
REVERT: B  149 GLU cc_start: 0.7060 (tp30) cc_final: 0.6773 (mm-30)
REVERT: B  191 GLU cc_start: 0.8288 (pm20) cc_final: 0.7893 (pm20)
REVERT: B  257 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6506 (mm)
REVERT: C  105 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.6787 (m-80)
REVERT: C  110 TRP cc_start: 0.6985 (p-90) cc_final: 0.6707 (p-90)
  outliers start: 28
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0883
  time to fit residues: 11.6963
Evaluate side-chains
  94 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   93 CYS
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  355 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0060
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0770
   chunk 41 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7758

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.206548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.164611 restraints weight = 7577.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 3.51
r_work: 0.3696 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   5776  Z= 0.156
  Angle     :  0.645  11.477   7875  Z= 0.319
  Chirality :  0.042   0.145    871
  Planarity :  0.005   0.058   1011
  Dihedral  :  5.738  55.601    766
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 27.77 %
    Favored  : 66.93 %
  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 aren not related in a simple way.
  whole: -1.09 (0.34), residues: 695
  helix:  1.92 (0.51), residues: 117
  sheet: -1.37 (0.42), residues: 166
  loop : -1.25 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 249 
 TYR   0.011   0.001   TYR C  69 
 PHE   0.024   0.002   PHE C 105 
 TRP   0.014   0.002   TRP B 198 
 HIS   0.001   0.000   HIS B 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 5765)
  covalent geometry    : angle       0.63545 ( 7853)
  SS BOND              : bond        0.00690 (   11)
  SS BOND              : angle       2.14323 (   22)
  hydrogen bonds       : bond        0.03641 (  137)
  hydrogen bonds       : angle       5.88500 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.7715 (p0) cc_final: 0.6796 (p0)
REVERT: A   78 GLN cc_start: 0.7180 (mp10) cc_final: 0.6926 (mp10)
REVERT: B   26 GLN cc_start: 0.6446 (mt0) cc_final: 0.6130 (mm-40)
REVERT: B   46 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7077 (tm-30)
REVERT: B  149 GLU cc_start: 0.7044 (tp30) cc_final: 0.6793 (mm-30)
REVERT: B  155 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7542 (mm-30)
REVERT: B  191 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7879 (pm20)
REVERT: B  257 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6484 (mm)
REVERT: C  105 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6807 (m-80)
REVERT: C  110 TRP cc_start: 0.7035 (p-90) cc_final: 0.6793 (p-90)
  outliers start: 33
  outliers final: 25
  residues processed: 102
  average time/residue: 0.0842
  time to fit residues: 11.1150
Evaluate side-chains
  98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   93 CYS
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain C residue  355 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0020
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.207715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.164526 restraints weight = 7524.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 3.24
r_work: 0.3726 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   5776  Z= 0.144
  Angle     :  0.630  11.452   7875  Z= 0.313
  Chirality :  0.042   0.140    871
  Planarity :  0.005   0.057   1011
  Dihedral  :  5.680  55.104    766
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 27.29 %
    Favored  : 66.93 %
  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 aren not related in a simple way.
  whole: -1.05 (0.34), residues: 695
  helix:  2.00 (0.51), residues: 117
  sheet: -1.32 (0.42), residues: 161
  loop : -1.26 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 249 
 TYR   0.028   0.002   TYR C 171 
 PHE   0.023   0.002   PHE C 105 
 TRP   0.012   0.002   TRP B 198 
 HIS   0.001   0.000   HIS B 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 5765)
  covalent geometry    : angle       0.62073 ( 7853)
  SS BOND              : bond        0.00658 (   11)
  SS BOND              : angle       2.09220 (   22)
  hydrogen bonds       : bond        0.03451 (  137)
  hydrogen bonds       : angle       5.79108 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 75
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.7686 (p0) cc_final: 0.6787 (p0)
REVERT: A   78 GLN cc_start: 0.7143 (mp10) cc_final: 0.6874 (mp10)
REVERT: B   26 GLN cc_start: 0.6438 (mt0) cc_final: 0.6131 (mm-40)
REVERT: B   46 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: B  149 GLU cc_start: 0.7045 (tp30) cc_final: 0.6817 (mm-30)
REVERT: B  155 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7508 (mm-30)
REVERT: B  191 GLU cc_start: 0.8259 (pm20) cc_final: 0.7865 (pm20)
REVERT: B  257 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6541 (mm)
REVERT: C  105 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6973 (m-80)
  outliers start: 36
  outliers final: 28
  residues processed: 109
  average time/residue: 0.0731
  time to fit residues: 10.4113
Evaluate side-chains
  101 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 70
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   93 CYS
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  353 ILE
Chi-restraints excluded: chain C residue  355 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 30 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0670
   chunk 11 optimal weight:    0.0000
   chunk 44 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0370
   chunk 52 optimal weight:    0.1980
   chunk 16 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.0798

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 GLN
C 367 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.212777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.171099 restraints weight = 7635.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.4114 rms_B_bonded: 3.29
r_work: 0.3792 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   5776  Z= 0.120
  Angle     :  0.637  11.174   7875  Z= 0.313
  Chirality :  0.041   0.144    871
  Planarity :  0.005   0.055   1011
  Dihedral  :  5.558  56.901    766
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 30.02 %
    Favored  : 66.77 %
  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 aren not related in a simple way.
  whole: -0.87 (0.35), residues: 695
  helix:  2.16 (0.52), residues: 117
  sheet: -1.32 (0.42), residues: 167
  loop : -1.07 (0.33), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  46 
 TYR   0.024   0.001   TYR C 171 
 PHE   0.017   0.001   PHE C 105 
 TRP   0.040   0.002   TRP C 110 
 HIS   0.001   0.000   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5765)
  covalent geometry    : angle       0.62966 ( 7853)
  SS BOND              : bond        0.00653 (   11)
  SS BOND              : angle       1.90961 (   22)
  hydrogen bonds       : bond        0.03116 (  137)
  hydrogen bonds       : angle       5.53897 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.7341 (p0) cc_final: 0.6424 (p0)
REVERT: A   78 GLN cc_start: 0.7084 (mp10) cc_final: 0.6784 (mp10)
REVERT: B   26 GLN cc_start: 0.6223 (mt0) cc_final: 0.5999 (mm-40)
REVERT: B   46 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6964 (tm-30)
REVERT: B  149 GLU cc_start: 0.6881 (tp30) cc_final: 0.6106 (mm-30)
REVERT: B  191 GLU cc_start: 0.8239 (pm20) cc_final: 0.7833 (pm20)
REVERT: C  105 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6711 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 92
  average time/residue: 0.0762
  time to fit residues: 9.0770
Evaluate side-chains
  89 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  352 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0270
   chunk 14 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0980
   chunk 44 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 367 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.211357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.168844 restraints weight = 7695.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 3.24
r_work: 0.3769 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   5776  Z= 0.129
  Angle     :  0.638  12.699   7875  Z= 0.314
  Chirality :  0.042   0.142    871
  Planarity :  0.005   0.055   1011
  Dihedral  :  5.516  56.065    766
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 30.50 %
    Favored  : 66.13 %
  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 aren not related in a simple way.
  whole: -0.82 (0.34), residues: 695
  helix:  2.18 (0.51), residues: 117
  sheet: -1.19 (0.44), residues: 155
  loop : -1.09 (0.33), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 102 
 TYR   0.022   0.001   TYR C  80 
 PHE   0.019   0.001   PHE C 105 
 TRP   0.010   0.001   TRP B 245 
 HIS   0.001   0.000   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5765)
  covalent geometry    : angle       0.63113 ( 7853)
  SS BOND              : bond        0.00730 (   11)
  SS BOND              : angle       1.92142 (   22)
  hydrogen bonds       : bond        0.03238 (  137)
  hydrogen bonds       : angle       5.51303 (  357)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.7427 (p0) cc_final: 0.6529 (p0)
REVERT: A   78 GLN cc_start: 0.7128 (mp10) cc_final: 0.6927 (mp10)
REVERT: A  167 GLU cc_start: 0.7109 (mp0) cc_final: 0.6803 (mp0)
REVERT: B   46 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6973 (tm-30)
REVERT: B  149 GLU cc_start: 0.6906 (tp30) cc_final: 0.6609 (mm-30)
REVERT: B  191 GLU cc_start: 0.8265 (pm20) cc_final: 0.7867 (pm20)
REVERT: C  105 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6712 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 97
  average time/residue: 0.0882
  time to fit residues: 11.0030
Evaluate side-chains
  92 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  161 ARG
Chi-restraints excluded: chain B residue   50 CYS
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  105 PHE
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  352 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    0.0020
   chunk 6 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0370
   chunk 33 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.4066

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 247 GLN
C 367 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.210635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.168522 restraints weight = 7501.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.4092 rms_B_bonded: 3.27
r_work: 0.3766 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   5776  Z= 0.129
  Angle     :  0.648  12.435   7875  Z= 0.320
  Chirality :  0.042   0.141    871
  Planarity :  0.005   0.055   1011
  Dihedral  :  5.521  55.300    766
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 30.50 %
    Favored  : 65.97 %
  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 aren not related in a simple way.
  whole: -0.88 (0.34), residues: 695
  helix:  2.00 (0.51), residues: 117
  sheet: -1.20 (0.44), residues: 155
  loop : -1.11 (0.33), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 102 
 TYR   0.018   0.001   TYR C 171 
 PHE   0.020   0.001   PHE C 105 
 TRP   0.014   0.001   TRP B 198 
 HIS   0.001   0.000   HIS B 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5765)
  covalent geometry    : angle       0.64090 ( 7853)
  SS BOND              : bond        0.00661 (   11)
  SS BOND              : angle       1.90956 (   22)
  hydrogen bonds       : bond        0.03269 (  137)
  hydrogen bonds       : angle       5.58027 (  357)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1631.91 seconds
wall clock time: 28 minutes 38.62 seconds (1718.62 seconds total)