Starting phenix.real_space_refine
on Fri Aug 22 15:29:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aza_15757/08_2025/8aza_15757.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aza_15757/08_2025/8aza_15757.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aza_15757/08_2025/8aza_15757.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aza_15757/08_2025/8aza_15757.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aza_15757/08_2025/8aza_15757.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aza_15757/08_2025/8aza_15757.cif"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.025
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
     Zn      1      6.06       5
     S      20      5.16       5
     C    3204      2.51       5
     N     872      2.21       5
     O     873      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4970
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 624
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 4, 'TRANS': 71}
    Chain: "A"
      Number of atoms: 2327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2327
          Classifications: {'peptide': 284}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 263}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 2018
          Classifications: {'peptide': 246}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 229}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    336  SG  CYS C 200      35.671  18.583  82.528  1.00273.60           S
  ATOM    359  SG  CYS C 203      39.057  18.926  84.298  1.00305.23           S
  ATOM    564  SG  CYS C 227      38.823  16.632  81.459  1.00267.04           S

  Time building chain proxies: 1.13, per 1000 atoms: 0.23
  Number of scatterers: 4970
  At special positions: 0
  Unit cell: (71.949, 76.911, 95.932, 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)
     Zn      1     29.99
     S      20     16.00
     O     873      8.00
     N     872      7.00
     C    3204      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 182.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 301 "
        pdb="ZN    ZN C 301 " - pdb=" NE2 HIS C 220 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C 227 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C 203 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C 200 "
      Number of angles added : 3


  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1166

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 8 sheets defined
      43.9% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'C' and resid 162 through 170
      removed outlier: 3.570A  pdb=" N   ARG C 166 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 188
    Processing helix  chain 'C' and resid 215 through 224
    Processing helix  chain 'C' and resid 227 through 234
    Processing helix  chain 'A' and resid 56 through 73
    Processing helix  chain 'A' and resid 103 through 107
    Processing helix  chain 'A' and resid 117 through 136
      removed outlier: 3.989A  pdb=" N   LEU A 125 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 4.012A  pdb=" N   MET A 193 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 4.066A  pdb=" N   ILE A 212 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 223 " --> pdb=" O   THR A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 243
      removed outlier: 4.093A  pdb=" N   MET A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   TYR A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER A 243 " --> pdb=" O   MET A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 273
    Processing helix  chain 'A' and resid 282 through 295
      Proline residue:  A 292  - end of helix
    Processing helix  chain 'A' and resid 298 through 313
      removed outlier: 3.847A  pdb=" N   ILE A 307 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLN A 308 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 16
      No H-bonds generated for 'chain 'B' and resid 14 through 16'
    Processing helix  chain 'B' and resid 60 through 73
    Processing helix  chain 'B' and resid 102 through 108
      removed outlier: 3.718A  pdb=" N   LEU B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 136
    Processing helix  chain 'B' and resid 164 through 168
      removed outlier: 4.541A  pdb=" N   LEU B 167 " --> pdb=" O   ASP B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 225
    Processing helix  chain 'B' and resid 261 through 273
    Processing helix  chain 'B' and resid 282 through 297
      Proline residue:  B 292  - end of helix
      removed outlier: 3.843A  pdb=" N   PHE B 297 " --> pdb=" O   VAL B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 314
      removed outlier: 3.625A  pdb=" N   PHE B 302 " --> pdb=" O   GLU B 298 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL B 306 " --> pdb=" O   PHE B 302 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ILE B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 189 through 191
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 23
      removed outlier: 4.777A  pdb=" N   ASP A  20 " --> pdb=" O   ARG A  36 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG A  36 " --> pdb=" O   ASP A  20 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   GLY A  92 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   CYS A  85 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   GLU A  96 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   ILE A  81 " --> pdb=" O   GLU A  96 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102
    Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143
      removed outlier: 3.719A  pdb=" N   LEU A 143 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 26
      removed outlier: 4.589A  pdb=" N   LEU B  21 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   SER B  34 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   TYR B  23 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  23 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86
      removed outlier: 3.639A  pdb=" N   GLY B  83 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 142 through 143
      removed outlier: 3.825A  pdb=" N   LEU B 143 " --> pdb=" O   LYS B 169 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 154

    197 hydrogen bonds defined for protein.
    564 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: 0.52

  Time building geometry restraints manager: 0.56 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: 1581
        1.34 -     1.46: 816
        1.46 -     1.58: 2673
        1.58 -     1.70: 1
        1.70 -     1.82: 31
  Bond restraints: 5102
  Sorted by residual:
  bond pdb=" CB  PRO C 181 "
       pdb=" CG  PRO C 181 "
    ideal  model  delta    sigma   weight residual
    1.492  1.577 -0.085 5.00e-02 4.00e+02 2.89e+00
  bond pdb=" CA  LEU A 309 "
       pdb=" C   LEU A 309 "
    ideal  model  delta    sigma   weight residual
    1.524  1.502  0.021 1.32e-02 5.74e+03 2.61e+00
  bond pdb=" C   LEU A 309 "
       pdb=" O   LEU A 309 "
    ideal  model  delta    sigma   weight residual
    1.236  1.217  0.019 1.22e-02 6.72e+03 2.38e+00
  bond pdb=" CG  PRO C 181 "
       pdb=" CD  PRO C 181 "
    ideal  model  delta    sigma   weight residual
    1.503  1.551 -0.048 3.40e-02 8.65e+02 1.98e+00
  bond pdb=" CB  LYS B  61 "
       pdb=" CG  LYS B  61 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.96e+00
  ... (remaining 5097 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 6727
        1.93 -     3.87: 148
        3.87 -     5.80: 27
        5.80 -     7.74: 13
        7.74 -     9.67: 6
  Bond angle restraints: 6921
  Sorted by residual:
  angle pdb=" N   ASP A 278 "
        pdb=" CA  ASP A 278 "
        pdb=" C   ASP A 278 "
      ideal   model   delta    sigma   weight residual
     111.28  117.77   -6.49 1.09e+00 8.42e-01 3.54e+01
  angle pdb=" C   ASN A 276 "
        pdb=" N   PRO A 277 "
        pdb=" CA  PRO A 277 "
      ideal   model   delta    sigma   weight residual
     119.87  124.81   -4.94 1.04e+00 9.25e-01 2.26e+01
  angle pdb=" N   PRO A 277 "
        pdb=" CA  PRO A 277 "
        pdb=" C   PRO A 277 "
      ideal   model   delta    sigma   weight residual
     114.03  119.01   -4.98 1.23e+00 6.61e-01 1.64e+01
  angle pdb=" CA  PRO C 181 "
        pdb=" N   PRO C 181 "
        pdb=" CD  PRO C 181 "
      ideal   model   delta    sigma   weight residual
     112.00  106.47    5.53 1.40e+00 5.10e-01 1.56e+01
  angle pdb=" CA  LYS B  61 "
        pdb=" CB  LYS B  61 "
        pdb=" CG  LYS B  61 "
      ideal   model   delta    sigma   weight residual
     114.10  121.79   -7.69 2.00e+00 2.50e-01 1.48e+01
  ... (remaining 6916 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 2606
       17.94 -    35.87: 339
       35.87 -    53.81: 101
       53.81 -    71.74: 20
       71.74 -    89.68: 7
  Dihedral angle restraints: 3073
    sinusoidal: 1286
      harmonic: 1787
  Sorted by residual:
  dihedral pdb=" C   ASP A 278 "
           pdb=" N   ASP A 278 "
           pdb=" CA  ASP A 278 "
           pdb=" CB  ASP A 278 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.29   10.69     0      2.50e+00 1.60e-01 1.83e+01
  dihedral pdb=" N   ASP A 278 "
           pdb=" C   ASP A 278 "
           pdb=" CA  ASP A 278 "
           pdb=" CB  ASP A 278 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.27  -10.47     0      2.50e+00 1.60e-01 1.75e+01
  dihedral pdb=" CA  MET A  98 "
           pdb=" C   MET A  98 "
           pdb=" N   PRO A  99 "
           pdb=" CA  PRO A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.14  -16.86     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 3070 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 697
       0.085 -    0.170: 58
       0.170 -    0.254: 2
       0.254 -    0.339: 1
       0.339 -    0.424: 1
  Chirality restraints: 759
  Sorted by residual:
  chirality pdb=" CA  ASP A 278 "
            pdb=" N   ASP A 278 "
            pdb=" C   ASP A 278 "
            pdb=" CB  ASP A 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.49e+00
  chirality pdb=" CB  VAL B 222 "
            pdb=" CA  VAL B 222 "
            pdb=" CG1 VAL B 222 "
            pdb=" CG2 VAL B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CA  GLU A 279 "
            pdb=" N   GLU A 279 "
            pdb=" C   GLU A 279 "
            pdb=" CB  GLU A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 756 not shown)

  Planarity restraints: 877
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 280 "    0.069 5.00e-02 4.00e+02   1.04e-01 1.74e+01
        pdb=" N   PRO B 281 "   -0.181 5.00e-02 4.00e+02
        pdb=" CA  PRO B 281 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO B 281 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 180 "    0.063 5.00e-02 4.00e+02   9.31e-02 1.39e+01
        pdb=" N   PRO C 181 "   -0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO C 181 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO C 181 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 308 "    0.011 2.00e-02 2.50e+03   2.31e-02 5.35e+00
        pdb=" C   GLN A 308 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLN A 308 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 309 "    0.013 2.00e-02 2.50e+03
  ... (remaining 874 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 525
        2.74 -     3.28: 5526
        3.28 -     3.82: 9009
        3.82 -     4.36: 10348
        4.36 -     4.90: 16487
  Nonbonded interactions: 41895
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 293 "
            pdb=" OG1 THR B 296 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OE1 GLU A 196 "
            pdb=" OG  SER A 207 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ASN A 234 "
            pdb=" NE2 GLN A 237 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" NH2 ARG A 247 "
            pdb=" O   TRP A 273 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" NE2 HIS A 136 "
            pdb=" OD2 ASP A 211 "
     model   vdw
     2.308 3.120
  ... (remaining 41890 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 'A' and (resid 8 through 49 or resid 59 through 171 or resid 206 through  \ 
228 or resid 247 through 314))
  selection = chain 'B'
}

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=0.00 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:             2.420
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.700
  Find NCS groups from input model:        0.060
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   5106  Z= 0.155
  Angle     :  0.763   9.671   6924  Z= 0.386
  Chirality :  0.049   0.424    759
  Planarity :  0.006   0.104    877
  Dihedral  : 17.832  89.676   1907
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 26.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 33.39 %
    Favored  : 65.87 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.75 (0.34), residues: 588
  helix: -0.08 (0.33), residues: 247
  sheet: -2.64 (0.61), residues: 63
  loop : -0.15 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  74 
 TYR   0.013   0.001   TYR B 134 
 PHE   0.014   0.001   PHE A 229 
 TRP   0.024   0.002   TRP B 220 
 HIS   0.004   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5102)
  covalent geometry    : angle       0.75788 ( 6921)
  hydrogen bonds       : bond        0.20300 (  197)
  hydrogen bonds       : angle       7.14050 (  564)
  metal coordination   : bond        0.02677 (    4)
  metal coordination   : angle       4.43187 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 MET cc_start: 0.8022 (ppp) cc_final: 0.7004 (ppp)
REVERT: B   61 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8807 (tppt)
  outliers start: 4
  outliers final: 4
  residues processed: 80
  average time/residue: 0.0755
  time to fit residues: 8.0597
Evaluate side-chains
  72 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  223 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.2980
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0970
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
C 209 ASN
A 136 HIS
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN
B  86 ASN
B 108 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.120611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.097345 restraints weight = 20929.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 8.38
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5106  Z= 0.127
  Angle     :  0.678  11.481   6924  Z= 0.325
  Chirality :  0.044   0.156    759
  Planarity :  0.005   0.072    877
  Dihedral  :  5.245  51.347    670
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 29.54 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.62 (0.34), residues: 588
  helix:  0.22 (0.33), residues: 247
  sheet: -2.90 (0.55), residues: 70
  loop : -0.10 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 171 
 TYR   0.016   0.001   TYR C 191 
 PHE   0.012   0.001   PHE A 229 
 TRP   0.015   0.001   TRP A 118 
 HIS   0.004   0.001   HIS B 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5102)
  covalent geometry    : angle       0.67128 ( 6921)
  hydrogen bonds       : bond        0.04093 (  197)
  hydrogen bonds       : angle       5.70126 (  564)
  metal coordination   : bond        0.02460 (    4)
  metal coordination   : angle       4.65449 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 MET cc_start: 0.8286 (ppp) cc_final: 0.7681 (ppp)
REVERT: A  276 ASN cc_start: 0.8316 (p0) cc_final: 0.8002 (p0)
REVERT: B  265 MET cc_start: 0.8443 (mmt) cc_final: 0.8081 (mmt)
REVERT: B  280 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6721 (tpp80)
  outliers start: 27
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0578
  time to fit residues: 7.5504
Evaluate side-chains
  84 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  251 ASN
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  280 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 57 optimal weight:    0.2980
   chunk 29 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  71 HIS
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN
B 108 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.113276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.092170 restraints weight = 21159.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 7.46
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5106  Z= 0.193
  Angle     :  0.718   9.978   6924  Z= 0.348
  Chirality :  0.047   0.249    759
  Planarity :  0.005   0.055    877
  Dihedral  :  4.901  46.113    664
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 24.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 29.36 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.54 (0.35), residues: 588
  helix:  0.24 (0.34), residues: 246
  sheet: -2.71 (0.63), residues: 58
  loop : -0.20 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  41 
 TYR   0.024   0.002   TYR C 191 
 PHE   0.012   0.001   PHE A 229 
 TRP   0.018   0.002   TRP A 118 
 HIS   0.005   0.001   HIS A 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 5102)
  covalent geometry    : angle       0.71061 ( 6921)
  hydrogen bonds       : bond        0.04257 (  197)
  hydrogen bonds       : angle       5.81707 (  564)
  metal coordination   : bond        0.01958 (    4)
  metal coordination   : angle       4.87727 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 MET cc_start: 0.8184 (ppp) cc_final: 0.7706 (ppp)
REVERT: A  220 TRP cc_start: 0.7099 (OUTLIER) cc_final: 0.6782 (t60)
REVERT: A  276 ASN cc_start: 0.8792 (p0) cc_final: 0.8559 (p0)
REVERT: B   98 MET cc_start: 0.2239 (ptp) cc_final: 0.1767 (ptp)
REVERT: B  265 MET cc_start: 0.8622 (mmt) cc_final: 0.7960 (mmm)
  outliers start: 31
  outliers final: 14
  residues processed: 101
  average time/residue: 0.0657
  time to fit residues: 9.0432
Evaluate side-chains
  83 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  133 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 17 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6340

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 145 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.116845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.094627 restraints weight = 20188.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.4149 rms_B_bonded: 7.75
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5106  Z= 0.124
  Angle     :  0.683  10.508   6924  Z= 0.320
  Chirality :  0.045   0.185    759
  Planarity :  0.005   0.054    877
  Dihedral  :  4.781  47.758    664
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 28.81 %
    Favored  : 65.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.44 (0.34), residues: 588
  helix:  0.36 (0.34), residues: 240
  sheet: -2.52 (0.65), residues: 57
  loop : -0.23 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 280 
 TYR   0.011   0.001   TYR B 134 
 PHE   0.012   0.001   PHE A 229 
 TRP   0.016   0.002   TRP B 220 
 HIS   0.004   0.001   HIS A 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5102)
  covalent geometry    : angle       0.67561 ( 6921)
  hydrogen bonds       : bond        0.03447 (  197)
  hydrogen bonds       : angle       5.44788 (  564)
  metal coordination   : bond        0.02362 (    4)
  metal coordination   : angle       4.97643 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 MET cc_start: 0.8247 (ppp) cc_final: 0.7908 (ppp)
REVERT: A  220 TRP cc_start: 0.7156 (OUTLIER) cc_final: 0.6788 (t60)
REVERT: A  270 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9006 (mm-30)
REVERT: A  275 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8335 (mm-40)
REVERT: B   98 MET cc_start: 0.2417 (OUTLIER) cc_final: 0.1771 (ptp)
REVERT: B  265 MET cc_start: 0.8561 (mmt) cc_final: 0.7998 (mmt)
  outliers start: 30
  outliers final: 13
  residues processed: 98
  average time/residue: 0.0543
  time to fit residues: 7.4158
Evaluate side-chains
  82 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain B residue   15 TYR
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  306 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0670
   chunk 39 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.7924

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.111108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.089768 restraints weight = 20602.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 7.43
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5106  Z= 0.199
  Angle     :  0.764  10.194   6924  Z= 0.364
  Chirality :  0.047   0.219    759
  Planarity :  0.005   0.054    877
  Dihedral  :  4.968  43.935    664
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 25.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 28.99 %
    Favored  : 65.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.65 (0.34), residues: 588
  helix:  0.17 (0.34), residues: 247
  sheet: -2.55 (0.66), residues: 58
  loop : -0.34 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  74 
 TYR   0.016   0.002   TYR C 191 
 PHE   0.015   0.001   PHE A  75 
 TRP   0.018   0.002   TRP B 220 
 HIS   0.007   0.001   HIS B 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 5102)
  covalent geometry    : angle       0.75616 ( 6921)
  hydrogen bonds       : bond        0.04266 (  197)
  hydrogen bonds       : angle       5.83220 (  564)
  metal coordination   : bond        0.02421 (    4)
  metal coordination   : angle       5.32260 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: C  183 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8693 (tm-30)
REVERT: A  220 TRP cc_start: 0.7134 (OUTLIER) cc_final: 0.6734 (t60)
REVERT: A  266 ILE cc_start: 0.5553 (OUTLIER) cc_final: 0.5348 (mm)
REVERT: A  275 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8349 (mm-40)
REVERT: B  265 MET cc_start: 0.8682 (mmt) cc_final: 0.8021 (mmt)
  outliers start: 28
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0558
  time to fit residues: 7.0252
Evaluate side-chains
  83 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  306 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 22 optimal weight:    0.0270
   chunk 48 optimal weight:    4.9990
   chunk 58 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.115196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.092997 restraints weight = 20599.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 7.81
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5106  Z= 0.131
  Angle     :  0.737  11.221   6924  Z= 0.342
  Chirality :  0.047   0.250    759
  Planarity :  0.005   0.053    877
  Dihedral  :  4.858  45.470    664
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 18.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 29.91 %
    Favored  : 65.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.51 (0.35), residues: 588
  helix:  0.24 (0.34), residues: 247
  sheet: -2.40 (0.68), residues: 57
  loop : -0.26 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 280 
 TYR   0.018   0.001   TYR C 191 
 PHE   0.012   0.001   PHE A 229 
 TRP   0.017   0.002   TRP B 220 
 HIS   0.003   0.001   HIS B 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5102)
  covalent geometry    : angle       0.72966 ( 6921)
  hydrogen bonds       : bond        0.03562 (  197)
  hydrogen bonds       : angle       5.47362 (  564)
  metal coordination   : bond        0.02687 (    4)
  metal coordination   : angle       5.19487 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  183 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8705 (tm-30)
REVERT: A   49 LEU cc_start: 0.7610 (pt) cc_final: 0.7260 (tp)
REVERT: A  220 TRP cc_start: 0.7095 (OUTLIER) cc_final: 0.6671 (t60)
REVERT: A  275 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8316 (mm-40)
REVERT: B  265 MET cc_start: 0.8558 (mmt) cc_final: 0.8015 (mmt)
  outliers start: 24
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0543
  time to fit residues: 6.8860
Evaluate side-chains
  83 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain B residue   15 TYR
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  306 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 6 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.114486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.092441 restraints weight = 20530.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 7.95
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5106  Z= 0.141
  Angle     :  0.763  15.212   6924  Z= 0.351
  Chirality :  0.047   0.214    759
  Planarity :  0.005   0.059    877
  Dihedral  :  4.793  44.754    664
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 20.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 29.91 %
    Favored  : 65.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.54 (0.35), residues: 588
  helix:  0.13 (0.34), residues: 241
  sheet: -2.36 (0.68), residues: 57
  loop : -0.19 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  74 
 TYR   0.018   0.002   TYR C 191 
 PHE   0.015   0.001   PHE A 229 
 TRP   0.017   0.002   TRP A 118 
 HIS   0.007   0.001   HIS B 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5102)
  covalent geometry    : angle       0.75549 ( 6921)
  hydrogen bonds       : bond        0.03549 (  197)
  hydrogen bonds       : angle       5.53214 (  564)
  metal coordination   : bond        0.02708 (    4)
  metal coordination   : angle       5.04965 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LEU cc_start: 0.7241 (pt) cc_final: 0.6886 (tp)
REVERT: A  220 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6744 (t60)
REVERT: A  275 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8243 (mm-40)
REVERT: B  146 ASP cc_start: 0.7981 (t0) cc_final: 0.7771 (p0)
REVERT: B  265 MET cc_start: 0.8540 (mmt) cc_final: 0.7969 (mmt)
  outliers start: 24
  outliers final: 17
  residues processed: 83
  average time/residue: 0.0529
  time to fit residues: 6.3121
Evaluate side-chains
  85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  207 LEU
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain B residue   15 TYR
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  306 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 50 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 47 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0870
   chunk 43 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.115014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.094622 restraints weight = 21362.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.4182 rms_B_bonded: 7.56
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5106  Z= 0.131
  Angle     :  0.769  16.214   6924  Z= 0.351
  Chirality :  0.047   0.287    759
  Planarity :  0.005   0.060    877
  Dihedral  :  4.726  45.111    664
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 30.46 %
    Favored  : 65.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.45 (0.35), residues: 588
  helix:  0.19 (0.34), residues: 240
  sheet: -2.34 (0.69), residues: 57
  loop : -0.12 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 280 
 TYR   0.019   0.001   TYR C 191 
 PHE   0.017   0.001   PHE A 229 
 TRP   0.017   0.002   TRP B 220 
 HIS   0.005   0.001   HIS B 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5102)
  covalent geometry    : angle       0.76210 ( 6921)
  hydrogen bonds       : bond        0.03348 (  197)
  hydrogen bonds       : angle       5.35075 (  564)
  metal coordination   : bond        0.02724 (    4)
  metal coordination   : angle       5.10822 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 TRP cc_start: 0.7182 (OUTLIER) cc_final: 0.6718 (t60)
REVERT: A  275 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7593 (mm-40)
REVERT: B  146 ASP cc_start: 0.7894 (t0) cc_final: 0.7250 (t0)
REVERT: B  265 MET cc_start: 0.8550 (mmt) cc_final: 0.7955 (mmt)
  outliers start: 21
  outliers final: 17
  residues processed: 81
  average time/residue: 0.0537
  time to fit residues: 6.2073
Evaluate side-chains
  84 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain B residue   15 TYR
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  306 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.114018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.093591 restraints weight = 21299.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.4153 rms_B_bonded: 7.49
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5106  Z= 0.137
  Angle     :  0.769  16.745   6924  Z= 0.351
  Chirality :  0.046   0.205    759
  Planarity :  0.005   0.084    877
  Dihedral  :  4.686  44.024    664
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 19.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 31.19 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.44 (0.35), residues: 588
  helix:  0.14 (0.34), residues: 241
  sheet: -2.26 (0.69), residues: 57
  loop : -0.07 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  74 
 TYR   0.018   0.002   TYR C 191 
 PHE   0.014   0.001   PHE A 229 
 TRP   0.020   0.002   TRP B 220 
 HIS   0.006   0.001   HIS B 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5102)
  covalent geometry    : angle       0.76132 ( 6921)
  hydrogen bonds       : bond        0.03423 (  197)
  hydrogen bonds       : angle       5.34863 (  564)
  metal coordination   : bond        0.02240 (    4)
  metal coordination   : angle       5.35507 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 TRP cc_start: 0.7129 (OUTLIER) cc_final: 0.6659 (t60)
REVERT: B  146 ASP cc_start: 0.7987 (t0) cc_final: 0.7323 (t0)
REVERT: B  265 MET cc_start: 0.8575 (mmt) cc_final: 0.7980 (mmt)
  outliers start: 20
  outliers final: 17
  residues processed: 80
  average time/residue: 0.0435
  time to fit residues: 5.0770
Evaluate side-chains
  83 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain B residue   15 TYR
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  306 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0870
   chunk 13 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7564

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.114000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.094120 restraints weight = 20841.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.4150 rms_B_bonded: 7.25
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   5106  Z= 0.136
  Angle     :  0.773  17.114   6924  Z= 0.351
  Chirality :  0.046   0.220    759
  Planarity :  0.006   0.085    877
  Dihedral  :  4.677  43.657    664
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 18.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 31.19 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.48 (0.35), residues: 588
  helix:  0.13 (0.34), residues: 241
  sheet: -2.25 (0.69), residues: 57
  loop : -0.12 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  74 
 TYR   0.018   0.001   TYR C 191 
 PHE   0.018   0.001   PHE A 229 
 TRP   0.023   0.002   TRP B 220 
 HIS   0.006   0.001   HIS B 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5102)
  covalent geometry    : angle       0.76556 ( 6921)
  hydrogen bonds       : bond        0.03364 (  197)
  hydrogen bonds       : angle       5.30413 (  564)
  metal coordination   : bond        0.03339 (    4)
  metal coordination   : angle       5.18921 (    3)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 TRP cc_start: 0.7246 (OUTLIER) cc_final: 0.6737 (t60)
REVERT: B  146 ASP cc_start: 0.7855 (t0) cc_final: 0.7251 (t0)
REVERT: B  265 MET cc_start: 0.8569 (mmt) cc_final: 0.8019 (mmm)
  outliers start: 20
  outliers final: 15
  residues processed: 79
  average time/residue: 0.0588
  time to fit residues: 6.6194
Evaluate side-chains
  82 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  170 TRP
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain B residue   15 TYR
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue  100 ASN
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  306 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.113822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.093772 restraints weight = 20931.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.4159 rms_B_bonded: 7.33
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5106  Z= 0.139
  Angle     :  0.779  16.827   6924  Z= 0.358
  Chirality :  0.046   0.221    759
  Planarity :  0.005   0.084    877
  Dihedral  :  4.761  46.548    664
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 31.74 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.46 (0.35), residues: 588
  helix:  0.13 (0.34), residues: 241
  sheet: -2.08 (0.71), residues: 56
  loop : -0.14 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  74 
 TYR   0.019   0.002   TYR C 191 
 PHE   0.017   0.001   PHE A 229 
 TRP   0.022   0.002   TRP B 220 
 HIS   0.006   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5102)
  covalent geometry    : angle       0.77139 ( 6921)
  hydrogen bonds       : bond        0.03409 (  197)
  hydrogen bonds       : angle       5.30014 (  564)
  metal coordination   : bond        0.02761 (    4)
  metal coordination   : angle       5.22979 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1506.24 seconds
wall clock time: 26 minutes 30.23 seconds (1590.23 seconds total)