Starting phenix.real_space_refine
on Thu Oct 22 21:37:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11wr_76140/10_2026/11wr_76140.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11wr_76140/10_2026/11wr_76140.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11wr_76140/10_2026/11wr_76140.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11wr_76140/10_2026/11wr_76140.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11wr_76140/10_2026/11wr_76140.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11wr_76140/10_2026/11wr_76140.map"
  }
  resolution = 3.56
  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      22      5.16       5
     C    3768      2.51       5
     N     965      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5843
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1766
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 216}
    Chain: "B"
      Number of atoms: 1579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1579
          Classifications: {'peptide': 210}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195}
    Chain: "C"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2498
          Classifications: {'peptide': 324}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 7, 'TRANS': 316}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 1.29, per 1000 atoms: 0.22
  Number of scatterers: 5843
  At special positions: 0
  Unit cell: (72.558, 78.396, 140.112, 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      22     16.00
     O    1088      8.00
     N     965      7.00
     C    3768      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 194 " 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: 0.35
  Conformation dependent library (CDL) restraints added in 203.0 milliseconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1378

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 14 sheets defined
      37.6% alpha, 30.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.534A  pdb=" N   ALA A  32 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 158
    Processing helix  chain 'B' and resid 26 through 30
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.755A  pdb=" N   GLU B  83 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 127
    Processing helix  chain 'B' and resid 182 through 187
      removed outlier: 3.623A  pdb=" N   LYS B 187 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 97
      removed outlier: 3.889A  pdb=" N   LEU C  95 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   THR C  96 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 123
      removed outlier: 4.029A  pdb=" N   LEU C 119 " --> pdb=" O   VAL C 115 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ALA C 120 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 133
    Processing helix  chain 'C' and resid 145 through 150
    Processing helix  chain 'C' and resid 151 through 156
    Processing helix  chain 'C' and resid 158 through 171
      removed outlier: 4.235A  pdb=" N   LYS C 169 " --> pdb=" O   GLU C 165 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA C 170 " --> pdb=" O   ALA C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 220
      removed outlier: 4.091A  pdb=" N   TYR C 186 " --> pdb=" O   PRO C 182 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER C 202 " --> pdb=" O   GLN C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 248
    Processing helix  chain 'C' and resid 256 through 261
      removed outlier: 3.882A  pdb=" N   TRP C 261 " --> pdb=" O   SER C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 282
      Proline residue:  C 269  - end of helix
    Processing helix  chain 'C' and resid 292 through 312
    Processing helix  chain 'C' and resid 318 through 323
    Processing helix  chain 'C' and resid 327 through 343
      removed outlier: 4.176A  pdb=" N   CYS C 340 " --> pdb=" O   ASP C 336 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLY C 341 " --> pdb=" O   ASP C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 346 through 353
    Processing helix  chain 'C' and resid 360 through 379
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4
      removed outlier: 3.610A  pdb=" N   ARG A   3 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.829A  pdb=" N   TRP A  33 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   MET A  34 " --> pdb=" O   ARG A  50 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ARG A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12
      removed outlier: 6.965A  pdb=" N   CYS A  92 " --> pdb=" O   TRP A 103 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   TRP A 103 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ARG A  94 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 17 through 21
      removed outlier: 3.589A  pdb=" N   LEU A  18 " --> pdb=" O   MET A  82 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP A  72 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 124
      removed outlier: 3.763A  pdb=" N   GLY A 139 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   TYR A 176 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 124
      removed outlier: 3.763A  pdb=" N   GLY A 139 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   TYR A 176 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 200
    Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 6
    Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 13
      removed outlier: 6.506A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 13
    Processing sheet with id=AB2, first strand: chain 'B' and resid 117 through 119
      removed outlier: 3.619A  pdb=" N   PHE B 119 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   VAL B 134 " --> pdb=" O   PHE B 119 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   TYR B 173 " --> pdb=" O   ASP B 139 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 117 through 119
      removed outlier: 3.619A  pdb=" N   PHE B 119 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   VAL B 134 " --> pdb=" O   PHE B 119 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   TYR B 173 " --> pdb=" O   ASP B 139 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 154 through 156
      removed outlier: 4.654A  pdb=" N   TRP B 149 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL B 203 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 154 through 156
      removed outlier: 4.654A  pdb=" N   TRP B 149 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)

    345 hydrogen bonds defined for protein.
    918 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: 0.84

  Time building geometry restraints manager: 0.49 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: 1811
        1.34 -     1.46: 1459
        1.46 -     1.58: 2693
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 5994
  Sorted by residual:
  bond pdb=" N   PHE C 159 "
       pdb=" CA  PHE C 159 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.43e+00
  bond pdb=" N   SER C 161 "
       pdb=" CA  SER C 161 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.44e+00
  bond pdb=" N   SER C 160 "
       pdb=" CA  SER C 160 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.028 1.23e-02 6.61e+03 5.34e+00
  bond pdb=" C   SER C 158 "
       pdb=" O   SER C 158 "
    ideal  model  delta    sigma   weight residual
    1.231  1.251 -0.020 9.50e-03 1.11e+04 4.30e+00
  bond pdb=" N   SER C 158 "
       pdb=" CA  SER C 158 "
    ideal  model  delta    sigma   weight residual
    1.465  1.489 -0.023 1.35e-02 5.49e+03 3.00e+00
  ... (remaining 5989 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 8040
        2.47 -     4.95: 106
        4.95 -     7.42: 10
        7.42 -     9.89: 3
        9.89 -    12.37: 1
  Bond angle restraints: 8160
  Sorted by residual:
  angle pdb=" CA  LEU C 196 "
        pdb=" CB  LEU C 196 "
        pdb=" CG  LEU C 196 "
      ideal   model   delta    sigma   weight residual
     116.30  128.67  -12.37 3.50e+00 8.16e-02 1.25e+01
  angle pdb=" CA  LEU C 291 "
        pdb=" CB  LEU C 291 "
        pdb=" CG  LEU C 291 "
      ideal   model   delta    sigma   weight residual
     116.30  125.95   -9.65 3.50e+00 8.16e-02 7.60e+00
  angle pdb=" CA  SER C 161 "
        pdb=" C   SER C 161 "
        pdb=" O   SER C 161 "
      ideal   model   delta    sigma   weight residual
     120.63  117.76    2.87 1.08e+00 8.57e-01 7.08e+00
  angle pdb=" CA  LEU B 181 "
        pdb=" CB  LEU B 181 "
        pdb=" CG  LEU B 181 "
      ideal   model   delta    sigma   weight residual
     116.30  125.04   -8.74 3.50e+00 8.16e-02 6.23e+00
  angle pdb=" C   VAL A 150 "
        pdb=" N   THR A 151 "
        pdb=" CA  THR A 151 "
      ideal   model   delta    sigma   weight residual
     122.82  126.32   -3.50 1.42e+00 4.96e-01 6.08e+00
  ... (remaining 8155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3044
       17.70 -    35.39: 322
       35.39 -    53.09: 98
       53.09 -    70.78: 7
       70.78 -    88.48: 7
  Dihedral angle restraints: 3478
    sinusoidal: 1306
      harmonic: 2172
  Sorted by residual:
  dihedral pdb=" CB  CYS A 140 "
           pdb=" SG  CYS A 140 "
           pdb=" SG  CYS A 196 "
           pdb=" CB  CYS A 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -145.14   59.14     1      1.00e+01 1.00e-02 4.68e+01
  dihedral pdb=" CA  THR C 345 "
           pdb=" C   THR C 345 "
           pdb=" N   VAL C 346 "
           pdb=" CA  VAL C 346 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CB  CYS B 135 "
           pdb=" SG  CYS B 135 "
           pdb=" SG  CYS B 194 "
           pdb=" CB  CYS B 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   65.61   27.39     1      1.00e+01 1.00e-02 1.08e+01
  ... (remaining 3475 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 651
       0.040 -    0.079: 199
       0.079 -    0.119: 67
       0.119 -    0.159: 4
       0.159 -    0.198: 4
  Chirality restraints: 925
  Sorted by residual:
  chirality pdb=" CG  LEU B 181 "
            pdb=" CB  LEU B 181 "
            pdb=" CD1 LEU B 181 "
            pdb=" CD2 LEU B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 9.82e-01
  chirality pdb=" CB  THR C 366 "
            pdb=" CA  THR C 366 "
            pdb=" OG1 THR C 366 "
            pdb=" CG2 THR C 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.52e-01
  chirality pdb=" CA  ASN B 129 "
            pdb=" N   ASN B 129 "
            pdb=" C   ASN B 129 "
            pdb=" CB  ASN B 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.17e-01
  ... (remaining 922 not shown)

  Planarity restraints: 1021
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 146 "   -0.031 5.00e-02 4.00e+02   4.63e-02 3.43e+00
        pdb=" N   PRO A 147 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 147 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 147 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 197 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.12e+00
        pdb=" C   ALA C 197 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ALA C 197 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLN C 198 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 379 "   -0.006 2.00e-02 2.50e+03   1.19e-02 1.42e+00
        pdb=" C   ILE C 379 "    0.021 2.00e-02 2.50e+03
        pdb=" O   ILE C 379 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LEU C 380 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1018 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 448
        2.73 -     3.27: 6026
        3.27 -     3.82: 9785
        3.82 -     4.36: 11083
        4.36 -     4.90: 19566
  Nonbonded interactions: 46908
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  92 "
            pdb=" OG  SER B  95A"
     model   vdw
     2.190 3.040
  nonbonded pdb=" NH2 ARG B  61 "
            pdb=" OD2 ASP B  82 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OD1 ASP B  82 "
            pdb=" OH  TYR B  86 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   GLU B 124 "
            pdb=" NE2 GLN B 127 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OE1 GLN B   6 "
            pdb=" OG1 THR B 102 "
     model   vdw
     2.266 3.040
  ... (remaining 46903 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.800
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.040
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
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   0.034   5998  Z= 0.185
  Angle     :  0.683  12.369   8168  Z= 0.351
  Chirality :  0.043   0.198    925
  Planarity :  0.004   0.046   1021
  Dihedral  : 16.014  88.476   2088
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.37 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 25.16 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.31), residues: 760
  helix:  1.14 (0.33), residues: 255
  sheet:  0.07 (0.43), residues: 159
  loop : -1.43 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 259 
 TYR   0.011   0.001   TYR B  36 
 PHE   0.014   0.002   PHE C 307 
 TRP   0.018   0.001   TRP A  47 
 HIS   0.003   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.19 ( 5994)
  covalent geometry    : angle       0.68255 /  0.35 ( 8160)
  SS BOND              : bond        0.00144 /  0.07 (    4)
  SS BOND              : angle       1.11503 /  0.55 (    8)
  hydrogen bonds       : bond        0.19280 / 13.11 (  301)
  hydrogen bonds       : angle       8.84047 /  6.00 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7871 (mtm110)
REVERT: B   52 ASN cc_start: 0.7836 (t0) cc_final: 0.7510 (t0)
REVERT: B   69 ASN cc_start: 0.8895 (p0) cc_final: 0.8554 (p0)
REVERT: C  148 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8268 (tt)
REVERT: C  158 SER cc_start: 0.9060 (t) cc_final: 0.8704 (p)
REVERT: C  212 PHE cc_start: 0.8378 (t80) cc_final: 0.7989 (t80)
REVERT: C  232 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5252 (tt0)
  outliers start: 20
  outliers final: 18
  residues processed: 108
  average time/residue: 0.0662
  time to fit residues: 9.7503
Evaluate side-chains
  110 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  163 ILE
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  331 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74]
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 199 ASN
A 200 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.176761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.134445 restraints weight = 8433.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.132567 restraints weight = 6006.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.134687 restraints weight = 5239.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.135757 restraints weight = 3989.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.136042 restraints weight = 3571.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5998  Z= 0.170
  Angle     :  0.649  10.136   8168  Z= 0.335
  Chirality :  0.043   0.199    925
  Planarity :  0.004   0.043   1021
  Dihedral  :  6.649  65.270    846
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.97 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 24.21 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.31), residues: 760
  helix:  1.18 (0.33), residues: 262
  sheet:  0.28 (0.43), residues: 159
  loop : -1.68 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 275 
 TYR   0.011   0.001   TYR B  36 
 PHE   0.014   0.001   PHE A 166 
 TRP   0.021   0.001   TRP A  47 
 HIS   0.007   0.001   HIS A 200 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.17 ( 5994)
  covalent geometry    : angle       0.64803 /  0.33 ( 8160)
  SS BOND              : bond        0.00320 /  0.16 (    4)
  SS BOND              : angle       1.28312 /  0.63 (    8)
  hydrogen bonds       : bond        0.04458 /  3.10 (  301)
  hydrogen bonds       : angle       5.97527 /  4.11 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  123 PRO cc_start: 0.8225 (Cg_endo) cc_final: 0.7853 (Cg_exo)
REVERT: B   52 ASN cc_start: 0.7936 (t0) cc_final: 0.7601 (t0)
REVERT: B   69 ASN cc_start: 0.8947 (p0) cc_final: 0.8645 (p0)
REVERT: B  204 GLU cc_start: 0.8199 (pp20) cc_final: 0.7983 (pp20)
REVERT: C   59 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.5019 (tp)
REVERT: C  148 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8300 (tt)
REVERT: C  158 SER cc_start: 0.8817 (t) cc_final: 0.8501 (t)
REVERT: C  212 PHE cc_start: 0.8390 (t80) cc_final: 0.8004 (t80)
  outliers start: 27
  outliers final: 11
  residues processed: 120
  average time/residue: 0.0618
  time to fit residues: 10.2198
Evaluate side-chains
  101 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [49, 2, 47, 36, 44, 72, 30, 75, 1, 43, 11]
   chunk 49 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.174789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.132091 restraints weight = 8285.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.130043 restraints weight = 5606.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131369 restraints weight = 5020.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.131957 restraints weight = 4205.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.132551 restraints weight = 3869.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   5998  Z= 0.245
  Angle     :  0.692  11.646   8168  Z= 0.351
  Chirality :  0.045   0.194    925
  Planarity :  0.004   0.043   1021
  Dihedral  :  6.181  56.151    830
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.63 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 25.00 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.31), residues: 760
  helix:  1.06 (0.32), residues: 265
  sheet:  0.32 (0.43), residues: 159
  loop : -1.74 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 275 
 TYR   0.013   0.001   TYR B  36 
 PHE   0.013   0.002   PHE A 166 
 TRP   0.021   0.001   TRP A  47 
 HIS   0.005   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00574 /  0.24 ( 5994)
  covalent geometry    : angle       0.69056 /  0.35 ( 8160)
  SS BOND              : bond        0.00628 /  0.31 (    4)
  SS BOND              : angle       1.35417 /  0.63 (    8)
  hydrogen bonds       : bond        0.04440 /  3.12 (  301)
  hydrogen bonds       : angle       5.54860 /  3.85 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 95
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8597 (mmtt)
REVERT: B   52 ASN cc_start: 0.8055 (t0) cc_final: 0.7651 (t0)
REVERT: C   59 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.5017 (tp)
REVERT: C   93 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7358 (tpp)
REVERT: C  119 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7657 (mt)
REVERT: C  148 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8407 (tt)
REVERT: C  158 SER cc_start: 0.8897 (t) cc_final: 0.8299 (p)
REVERT: C  212 PHE cc_start: 0.8405 (t80) cc_final: 0.8044 (t80)
  outliers start: 35
  outliers final: 20
  residues processed: 121
  average time/residue: 0.0620
  time to fit residues: 10.3265
Evaluate side-chains
  113 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  135 ASP
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  361 SER
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [73, 72, 56, 59, 30, 74, 13, 69, 70, 6, 4]
   chunk 73 optimal weight:    0.4980
   chunk 72 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0980
   chunk 59 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0980
   overall best weight:    0.5180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.175444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.133513 restraints weight = 8118.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.132742 restraints weight = 5221.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.134995 restraints weight = 4359.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.135374 restraints weight = 3670.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.135838 restraints weight = 3288.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5998  Z= 0.141
  Angle     :  0.628   9.854   8168  Z= 0.318
  Chirality :  0.042   0.180    925
  Planarity :  0.004   0.039   1021
  Dihedral  :  5.693  58.735    828
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.45 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 25.94 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.32), residues: 760
  helix:  1.27 (0.33), residues: 263
  sheet:  0.33 (0.41), residues: 171
  loop : -1.62 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  83 
 TYR   0.011   0.001   TYR B  36 
 PHE   0.011   0.001   PHE A 166 
 TRP   0.009   0.001   TRP B 149 
 HIS   0.002   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 5994)
  covalent geometry    : angle       0.62713 /  0.32 ( 8160)
  SS BOND              : bond        0.00277 /  0.14 (    4)
  SS BOND              : angle       1.15900 /  0.53 (    8)
  hydrogen bonds       : bond        0.03821 /  2.63 (  301)
  hydrogen bonds       : angle       5.18457 /  3.58 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8399 (pp)
REVERT: A   83 ARG cc_start: 0.8225 (mtm110) cc_final: 0.8020 (mtm110)
REVERT: A  123 PRO cc_start: 0.8333 (Cg_endo) cc_final: 0.7855 (Cg_exo)
REVERT: A  201 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8562 (mmtt)
REVERT: B   52 ASN cc_start: 0.7968 (t0) cc_final: 0.7533 (t0)
REVERT: B   69 ASN cc_start: 0.8921 (p0) cc_final: 0.8615 (p0)
REVERT: C   59 LEU cc_start: 0.5064 (OUTLIER) cc_final: 0.4753 (tp)
REVERT: C  117 MET cc_start: 0.8461 (tpp) cc_final: 0.8116 (tpp)
REVERT: C  121 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7367 (tp)
REVERT: C  148 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8458 (tt)
REVERT: C  158 SER cc_start: 0.8816 (t) cc_final: 0.8489 (t)
REVERT: C  212 PHE cc_start: 0.8365 (t80) cc_final: 0.7994 (t80)
  outliers start: 25
  outliers final: 15
  residues processed: 111
  average time/residue: 0.0667
  time to fit residues: 10.0167
Evaluate side-chains
  105 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  157 SER
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  361 SER
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [4, 13, 2, 43, 61, 56, 23, 31, 12, 8, 16]
   chunk 4 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.174913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.132697 restraints weight = 8358.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.130823 restraints weight = 5401.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.132344 restraints weight = 4742.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.132834 restraints weight = 3918.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.133523 restraints weight = 3627.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5998  Z= 0.176
  Angle     :  0.636   9.463   8168  Z= 0.322
  Chirality :  0.043   0.180    925
  Planarity :  0.004   0.038   1021
  Dihedral  :  5.552  58.823    826
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.24 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 26.26 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.32), residues: 760
  helix:  1.24 (0.33), residues: 263
  sheet:  0.28 (0.40), residues: 178
  loop : -1.60 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  83 
 TYR   0.011   0.001   TYR B  36 
 PHE   0.010   0.001   PHE A 166 
 TRP   0.010   0.001   TRP A  47 
 HIS   0.004   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.18 ( 5994)
  covalent geometry    : angle       0.63536 /  0.32 ( 8160)
  SS BOND              : bond        0.00262 /  0.13 (    4)
  SS BOND              : angle       1.14864 /  0.51 (    8)
  hydrogen bonds       : bond        0.03885 /  2.69 (  301)
  hydrogen bonds       : angle       5.09133 /  3.52 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8396 (pp)
REVERT: A  201 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8560 (mmtt)
REVERT: B   52 ASN cc_start: 0.8039 (t0) cc_final: 0.7607 (t0)
REVERT: C   59 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4785 (tp)
REVERT: C  158 SER cc_start: 0.8889 (t) cc_final: 0.8484 (t)
REVERT: C  212 PHE cc_start: 0.8357 (t80) cc_final: 0.7974 (t80)
  outliers start: 32
  outliers final: 24
  residues processed: 114
  average time/residue: 0.0657
  time to fit residues: 10.3014
Evaluate side-chains
  108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  135 ASP
Chi-restraints excluded: chain C residue  157 SER
Chi-restraints excluded: chain C residue  169 LYS
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  361 SER
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [29, 7, 10, 5, 44, 58, 43, 24, 74, 13, 47]
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.173872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.131316 restraints weight = 8321.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.128999 restraints weight = 5606.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.130762 restraints weight = 5405.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131638 restraints weight = 4392.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131511 restraints weight = 4080.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5998  Z= 0.231
  Angle     :  0.680   9.962   8168  Z= 0.342
  Chirality :  0.044   0.183    925
  Planarity :  0.005   0.075   1021
  Dihedral  :  5.374  58.829    824
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.37 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 25.94 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.32), residues: 760
  helix:  1.08 (0.32), residues: 266
  sheet:  0.24 (0.40), residues: 178
  loop : -1.64 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  83 
 TYR   0.013   0.001   TYR B  36 
 PHE   0.012   0.002   PHE B 140 
 TRP   0.012   0.001   TRP A  47 
 HIS   0.004   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00545 /  0.23 ( 5994)
  covalent geometry    : angle       0.67965 /  0.34 ( 8160)
  SS BOND              : bond        0.00277 /  0.14 (    4)
  SS BOND              : angle       1.23265 /  0.56 (    8)
  hydrogen bonds       : bond        0.04111 /  2.89 (  301)
  hydrogen bonds       : angle       5.14335 /  3.57 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 87
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8466 (pp)
REVERT: A  201 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8607 (mmtt)
REVERT: B   52 ASN cc_start: 0.8057 (t0) cc_final: 0.7643 (t0)
REVERT: C   64 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6843 (t0)
REVERT: C   93 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7483 (tpp)
REVERT: C  158 SER cc_start: 0.8944 (t) cc_final: 0.8510 (t)
REVERT: C  212 PHE cc_start: 0.8403 (t80) cc_final: 0.8024 (t80)
  outliers start: 35
  outliers final: 25
  residues processed: 114
  average time/residue: 0.0694
  time to fit residues: 10.7756
Evaluate side-chains
  111 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  135 ASP
Chi-restraints excluded: chain C residue  157 SER
Chi-restraints excluded: chain C residue  169 LYS
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  361 SER
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [47, 11, 53, 52, 67, 42, 63, 39, 23, 31, 69]
   chunk 47 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 63 optimal weight:   20.0000
   chunk 39 optimal weight:    0.4980
   chunk 23 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.174999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.132926 restraints weight = 8234.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.131310 restraints weight = 5295.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.132458 restraints weight = 4728.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.133102 restraints weight = 3965.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.133714 restraints weight = 3648.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5998  Z= 0.155
  Angle     :  0.670  10.701   8168  Z= 0.330
  Chirality :  0.043   0.174    925
  Planarity :  0.004   0.068   1021
  Dihedral  :  5.136  55.408    824
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.18 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 26.26 %
    Favored  : 68.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.32), residues: 760
  helix:  1.24 (0.33), residues: 264
  sheet:  0.35 (0.42), residues: 168
  loop : -1.59 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  83 
 TYR   0.012   0.001   TYR B  36 
 PHE   0.008   0.001   PHE C 191 
 TRP   0.012   0.001   TRP A  47 
 HIS   0.003   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 ( 5994)
  covalent geometry    : angle       0.66947 /  0.33 ( 8160)
  SS BOND              : bond        0.00268 /  0.13 (    4)
  SS BOND              : angle       1.06228 /  0.47 (    8)
  hydrogen bonds       : bond        0.03772 /  2.61 (  301)
  hydrogen bonds       : angle       4.94706 /  3.41 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8433 (pp)
REVERT: A  201 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8587 (mmtt)
REVERT: B   52 ASN cc_start: 0.8038 (t0) cc_final: 0.7616 (t0)
REVERT: C  121 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7419 (tp)
REVERT: C  158 SER cc_start: 0.8884 (t) cc_final: 0.8463 (t)
REVERT: C  212 PHE cc_start: 0.8361 (t80) cc_final: 0.7994 (t80)
REVERT: C  232 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5954 (tp30)
  outliers start: 31
  outliers final: 22
  residues processed: 110
  average time/residue: 0.0713
  time to fit residues: 10.5134
Evaluate side-chains
  110 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   82 ASN
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  135 ASP
Chi-restraints excluded: chain C residue  169 LYS
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  361 SER
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [44, 7, 10, 32, 67, 24, 59, 68, 70, 37, 11]
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0870
   overall best weight:    0.6962

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.176966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.134475 restraints weight = 8277.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.132181 restraints weight = 5545.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.133983 restraints weight = 5280.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.134545 restraints weight = 4324.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.134712 restraints weight = 3727.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5998  Z= 0.158
  Angle     :  0.661  10.104   8168  Z= 0.327
  Chirality :  0.042   0.175    925
  Planarity :  0.004   0.064   1021
  Dihedral  :  5.019  52.353    824
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.71 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 25.94 %
    Favored  : 69.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.32), residues: 760
  helix:  1.25 (0.33), residues: 262
  sheet:  0.34 (0.42), residues: 162
  loop : -1.47 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  83 
 TYR   0.011   0.001   TYR B  36 
 PHE   0.009   0.001   PHE C 191 
 TRP   0.016   0.001   TRP C  68 
 HIS   0.003   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.16 ( 5994)
  covalent geometry    : angle       0.66016 /  0.33 ( 8160)
  SS BOND              : bond        0.00238 /  0.12 (    4)
  SS BOND              : angle       1.04478 /  0.46 (    8)
  hydrogen bonds       : bond        0.03733 /  2.58 (  301)
  hydrogen bonds       : angle       4.86769 /  3.36 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 87
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   35 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8849 (m)
REVERT: A   45 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8430 (pp)
REVERT: A  201 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8579 (mmtt)
REVERT: B   52 ASN cc_start: 0.8010 (t0) cc_final: 0.7580 (t0)
REVERT: C  121 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7423 (tp)
REVERT: C  158 SER cc_start: 0.8909 (t) cc_final: 0.8484 (t)
REVERT: C  212 PHE cc_start: 0.8368 (t80) cc_final: 0.8012 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 109
  average time/residue: 0.0623
  time to fit residues: 9.4357
Evaluate side-chains
  114 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   82 ASN
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  135 ASP
Chi-restraints excluded: chain C residue  169 LYS
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  361 SER
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [34, 70, 61, 24, 22, 56, 55, 15, 19, 13, 63]
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0270
   chunk 61 optimal weight:    0.8980
   chunk 24 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    0.8040

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.176188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.133671 restraints weight = 8365.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.131715 restraints weight = 5549.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.133386 restraints weight = 5306.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.134063 restraints weight = 4246.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.134216 restraints weight = 3714.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5998  Z= 0.170
  Angle     :  0.671  13.241   8168  Z= 0.332
  Chirality :  0.043   0.175    925
  Planarity :  0.004   0.063   1021
  Dihedral  :  4.566  34.506    821
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.97 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 25.94 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.31), residues: 760
  helix:  1.16 (0.32), residues: 265
  sheet:  0.38 (0.43), residues: 157
  loop : -1.45 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  83 
 TYR   0.011   0.001   TYR B  36 
 PHE   0.009   0.001   PHE A 122 
 TRP   0.013   0.001   TRP A  47 
 HIS   0.003   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.17 ( 5994)
  covalent geometry    : angle       0.67099 /  0.33 ( 8160)
  SS BOND              : bond        0.00265 /  0.13 (    4)
  SS BOND              : angle       1.03632 /  0.45 (    8)
  hydrogen bonds       : bond        0.03786 /  2.63 (  301)
  hydrogen bonds       : angle       4.83631 /  3.34 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8436 (pp)
REVERT: A   72 ASP cc_start: 0.7386 (t0) cc_final: 0.7112 (t0)
REVERT: A  201 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8581 (mmtt)
REVERT: B   52 ASN cc_start: 0.8029 (t0) cc_final: 0.7608 (t0)
REVERT: C  158 SER cc_start: 0.8937 (t) cc_final: 0.8508 (t)
REVERT: C  212 PHE cc_start: 0.8358 (t80) cc_final: 0.7964 (t80)
  outliers start: 28
  outliers final: 27
  residues processed: 107
  average time/residue: 0.0610
  time to fit residues: 9.1571
Evaluate side-chains
  113 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 85
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   82 ASN
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain C residue  135 ASP
Chi-restraints excluded: chain C residue  169 LYS
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  361 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [56, 58, 10, 34, 41, 17, 42, 49, 70, 45, 39]
   chunk 56 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 70 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.1584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.174321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.131702 restraints weight = 8461.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.128934 restraints weight = 5674.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130326 restraints weight = 5239.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131114 restraints weight = 4558.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.131176 restraints weight = 4245.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5998  Z= 0.216
  Angle     :  0.705  14.327   8168  Z= 0.350
  Chirality :  0.044   0.176    925
  Planarity :  0.004   0.063   1021
  Dihedral  :  4.667  32.654    821
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.24 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 25.79 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.31), residues: 760
  helix:  1.07 (0.32), residues: 264
  sheet:  0.41 (0.42), residues: 168
  loop : -1.56 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 275 
 TYR   0.013   0.001   TYR B  86 
 PHE   0.013   0.002   PHE C 373 
 TRP   0.014   0.001   TRP A  47 
 HIS   0.004   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00507 /  0.22 ( 5994)
  covalent geometry    : angle       0.70429 /  0.35 ( 8160)
  SS BOND              : bond        0.00254 /  0.13 (    4)
  SS BOND              : angle       1.18667 /  0.52 (    8)
  hydrogen bonds       : bond        0.03989 /  2.80 (  301)
  hydrogen bonds       : angle       4.94833 /  3.42 (  918)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 87
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8504 (pp)
REVERT: A  201 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8612 (mmtt)
REVERT: B   52 ASN cc_start: 0.8066 (t0) cc_final: 0.7667 (t0)
REVERT: C  158 SER cc_start: 0.8974 (t) cc_final: 0.8545 (t)
REVERT: C  212 PHE cc_start: 0.8356 (t80) cc_final: 0.7999 (t80)
  outliers start: 29
  outliers final: 28
  residues processed: 107
  average time/residue: 0.0653
  time to fit residues: 9.6843
Evaluate side-chains
  113 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   82 ASN
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  128 ILE
Chi-restraints excluded: chain C residue  135 ASP
Chi-restraints excluded: chain C residue  169 LYS
Chi-restraints excluded: chain C residue  208 MET
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  361 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [49, 44, 64, 60, 16, 61, 66, 43, 72, 63, 26]
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 64 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.177026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.134587 restraints weight = 8297.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.132688 restraints weight = 5593.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.134356 restraints weight = 5322.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135043 restraints weight = 4257.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.135197 restraints weight = 3703.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5998  Z= 0.151
  Angle     :  0.679  14.495   8168  Z= 0.333
  Chirality :  0.043   0.174    925
  Planarity :  0.004   0.063   1021
  Dihedral  :  4.512  30.653    821
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.84 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 26.10 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.31), residues: 760
  helix:  1.30 (0.32), residues: 259
  sheet:  0.42 (0.43), residues: 157
  loop : -1.41 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  83 
 TYR   0.041   0.001   TYR B  49 
 PHE   0.012   0.001   PHE C 191 
 TRP   0.012   0.001   TRP C  68 
 HIS   0.003   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 ( 5994)
  covalent geometry    : angle       0.67863 /  0.33 ( 8160)
  SS BOND              : bond        0.00214 /  0.11 (    4)
  SS BOND              : angle       0.97919 /  0.43 (    8)
  hydrogen bonds       : bond        0.03662 /  2.54 (  301)
  hydrogen bonds       : angle       4.81290 /  3.32 (  918)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1043.41 seconds
wall clock time: 18 minutes 48.05 seconds (1128.05 seconds total)