Starting phenix.real_space_refine
on Sun Apr  5 16:55:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r2n_53533/04_2026/9r2n_53533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r2n_53533/04_2026/9r2n_53533.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r2n_53533/04_2026/9r2n_53533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r2n_53533/04_2026/9r2n_53533.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r2n_53533/04_2026/9r2n_53533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r2n_53533/04_2026/9r2n_53533.cif"
  }
  resolution = 3.83
  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=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     C    3680      2.51       5
     N     990      2.21       5
     O    1138      1.98       5
     H    5802      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11639
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 3826
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 4, 'TRANS': 233}
    Chain: "B"
      Number of atoms: 3768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 3768
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 4, 'TRANS': 229}
    Chain: "D"
      Number of atoms: 4045
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 4045
          Classifications: {'peptide': 247}
          Link IDs: {'PTRANS': 12, 'TRANS': 234}
  Time building chain proxies: 2.16, per 1000 atoms: 0.19
  Number of scatterers: 11639
  At special positions: 0
  Unit cell: (78.3584, 86.6944, 114.203, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      27     16.00
     P       2     15.00
     O    1138      8.00
     N     990      7.00
     C    3680      6.00
     H    5802      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 358.2 milliseconds
  

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      78.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 19 through 33
    Processing helix  chain 'A' and resid 38 through 74
      removed outlier: 3.863A  pdb=" N   ALA A  55 " --> pdb=" O   ASN A  51 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ARG A  56 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 107
    Processing helix  chain 'A' and resid 107 through 112
    Processing helix  chain 'A' and resid 116 through 138
      removed outlier: 3.793A  pdb=" N   VAL A 137 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 164
      removed outlier: 3.865A  pdb=" N   GLU A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN A 164 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 186
    Processing helix  chain 'A' and resid 189 through 207
    Processing helix  chain 'A' and resid 215 through 234
    Processing helix  chain 'B' and resid 4 through 17
    Processing helix  chain 'B' and resid 19 through 32
      removed outlier: 3.810A  pdb=" N   MET B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 74
      removed outlier: 3.702A  pdb=" N   ARG B  56 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 107
    Processing helix  chain 'B' and resid 107 through 112
    Processing helix  chain 'B' and resid 116 through 138
      removed outlier: 3.883A  pdb=" N   VAL B 137 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 165
    Processing helix  chain 'B' and resid 169 through 185
    Processing helix  chain 'B' and resid 189 through 207
      removed outlier: 3.660A  pdb=" N   GLU B 207 " --> pdb=" O   ASP B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 212
      removed outlier: 3.620A  pdb=" N   ASN B 212 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 235
      removed outlier: 3.519A  pdb=" N   TRP B 233 " --> pdb=" O   ASN B 229 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR B 234 " --> pdb=" O   LEU B 230 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 133
    Processing helix  chain 'D' and resid 142 through 146
      removed outlier: 4.101A  pdb=" N   PHE D 145 " --> pdb=" O   LEU D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 163
      removed outlier: 4.560A  pdb=" N   ASP D 162 " --> pdb=" O   PRO D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 183
    Processing helix  chain 'D' and resid 185 through 204
    Processing helix  chain 'D' and resid 208 through 211
    Processing helix  chain 'D' and resid 212 through 228
    Processing helix  chain 'D' and resid 245 through 261
    Processing helix  chain 'D' and resid 267 through 284
    Processing helix  chain 'D' and resid 295 through 303
    Processing helix  chain 'D' and resid 305 through 310

    425 hydrogen bonds defined for protein.
    1260 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: 2.35

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        0.86 -     1.05: 1908
        1.05 -     1.24: 4661
        1.24 -     1.43: 1704
        1.43 -     1.62: 3421
        1.62 -     1.81: 42
  Bond restraints: 11736
  Sorted by residual:
  bond pdb=" N   SEP D 100 "
       pdb=" H   SEP D 100 "
    ideal  model  delta    sigma   weight residual
    0.860  1.089 -0.229 2.00e-02 2.50e+03 1.31e+02
  bond pdb=" N   SEP D 326 "
       pdb=" H   SEP D 326 "
    ideal  model  delta    sigma   weight residual
    0.860  1.089 -0.229 2.00e-02 2.50e+03 1.31e+02
  bond pdb=" NE1 TRP D 212 "
       pdb=" HE1 TRP D 212 "
    ideal  model  delta    sigma   weight residual
    0.860  1.082 -0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" NE1 TRP D 233 "
       pdb=" HE1 TRP D 233 "
    ideal  model  delta    sigma   weight residual
    0.860  1.082 -0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" NE1 TRP A 233 "
       pdb=" HE1 TRP A 233 "
    ideal  model  delta    sigma   weight residual
    0.860  1.082 -0.222 2.00e-02 2.50e+03 1.23e+02
  ... (remaining 11731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 18080
        1.25 -     2.50: 1892
        2.50 -     3.74: 1178
        3.74 -     4.99: 47
        4.99 -     6.24: 18
  Bond angle restraints: 21215
  Sorted by residual:
  angle pdb=" CA  ASP D 137 "
        pdb=" C   ASP D 137 "
        pdb=" O   ASP D 137 "
      ideal   model   delta    sigma   weight residual
     120.55  117.43    3.12 1.06e+00 8.90e-01 8.66e+00
  angle pdb=" C   LEU D 316 "
        pdb=" N   ARG D 317 "
        pdb=" CA  ARG D 317 "
      ideal   model   delta    sigma   weight residual
     121.54  127.16   -5.62 1.91e+00 2.74e-01 8.65e+00
  angle pdb=" CA  LEU D 141 "
        pdb=" C   LEU D 141 "
        pdb=" O   LEU D 141 "
      ideal   model   delta    sigma   weight residual
     121.84  118.43    3.41 1.16e+00 7.43e-01 8.64e+00
  angle pdb=" CA  LEU D 142 "
        pdb=" C   LEU D 142 "
        pdb=" O   LEU D 142 "
      ideal   model   delta    sigma   weight residual
     120.92  118.03    2.89 1.14e+00 7.69e-01 6.43e+00
  angle pdb=" CA  ASP D 135 "
        pdb=" CB  ASP D 135 "
        pdb=" CG  ASP D 135 "
      ideal   model   delta    sigma   weight residual
     112.60  115.03   -2.43 1.00e+00 1.00e+00 5.93e+00
  ... (remaining 21210 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.71: 5191
       13.71 -    27.43: 199
       27.43 -    41.14: 58
       41.14 -    54.85: 38
       54.85 -    68.56: 5
  Dihedral angle restraints: 5491
    sinusoidal: 3007
      harmonic: 2484
  Sorted by residual:
  dihedral pdb=" N   MET D 140 "
           pdb=" CA  MET D 140 "
           pdb=" CB  MET D 140 "
           pdb=" CG  MET D 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.82  -53.18     3      1.50e+01 4.44e-03 9.18e+00
  dihedral pdb=" N   PHE D 145 "
           pdb=" CA  PHE D 145 "
           pdb=" CB  PHE D 145 "
           pdb=" CG  PHE D 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -7.06  -52.94     3      1.50e+01 4.44e-03 9.16e+00
  dihedral pdb=" CA  ARG D 317 "
           pdb=" CB  ARG D 317 "
           pdb=" CG  ARG D 317 "
           pdb=" CD  ARG D 317 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.13   50.13     3      1.50e+01 4.44e-03 8.86e+00
  ... (remaining 5488 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 605
       0.023 -    0.046: 171
       0.046 -    0.068: 69
       0.068 -    0.091: 30
       0.091 -    0.114: 15
  Chirality restraints: 890
  Sorted by residual:
  chirality pdb=" CA  LEU D 142 "
            pdb=" N   LEU D 142 "
            pdb=" C   LEU D 142 "
            pdb=" CB  LEU D 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.62   -0.11 2.00e-01 2.50e+01 3.23e-01
  chirality pdb=" CA  VAL D 157 "
            pdb=" N   VAL D 157 "
            pdb=" C   VAL D 157 "
            pdb=" CB  VAL D 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.07e-01
  chirality pdb=" CA  ILE D 305 "
            pdb=" N   ILE D 305 "
            pdb=" C   ILE D 305 "
            pdb=" CB  ILE D 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.01e-01
  ... (remaining 887 not shown)

  Planarity restraints: 1731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 139 "    0.503 9.50e-02 1.11e+02   3.64e-01 2.38e+03
        pdb=" NE  ARG D 139 "    0.384 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 139 "    0.081 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 139 "   -0.059 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 139 "   -0.050 2.00e-02 2.50e+03
        pdb="HH11 ARG D 139 "   -0.443 2.00e-02 2.50e+03
        pdb="HH12 ARG D 139 "    0.240 2.00e-02 2.50e+03
        pdb="HH21 ARG D 139 "   -0.593 2.00e-02 2.50e+03
        pdb="HH22 ARG D 139 "    0.419 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  99 "    0.060 2.00e-02 2.50e+03   1.01e-01 1.02e+02
        pdb=" N   SEP D 100 "   -0.174 2.00e-02 2.50e+03
        pdb=" CA  SEP D 100 "    0.049 2.00e-02 2.50e+03
        pdb=" H   SEP D 100 "    0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 325 "   -0.029 2.00e-02 2.50e+03   4.78e-02 2.28e+01
        pdb=" N   SEP D 326 "    0.083 2.00e-02 2.50e+03
        pdb=" CA  SEP D 326 "   -0.022 2.00e-02 2.50e+03
        pdb=" H   SEP D 326 "   -0.032 2.00e-02 2.50e+03
  ... (remaining 1728 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 628
        2.14 -     2.76: 22126
        2.76 -     3.37: 32144
        3.37 -     3.99: 41802
        3.99 -     4.60: 64818
  Nonbonded interactions: 161518
  Sorted by model distance:
  nonbonded pdb="HD22 ASN A 229 "
            pdb=" O   ALA D  99 "
     model   vdw
     1.528 2.450
  nonbonded pdb=" HZ3 LYS A  28 "
            pdb=" OE2 GLU A  32 "
     model   vdw
     1.544 2.450
  nonbonded pdb=" OE1 GLU B 118 "
            pdb=" H   GLU B 118 "
     model   vdw
     1.552 2.450
  nonbonded pdb=" O   VAL B  47 "
            pdb="HD21 ASN B  51 "
     model   vdw
     1.556 2.450
  nonbonded pdb=" OE1 GLU A 191 "
            pdb=" H   GLU A 191 "
     model   vdw
     1.569 2.450
  ... (remaining 161513 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 3 through 236)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.080
  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:             0.060
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.740
  Find NCS groups from input model:        0.090
  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:0.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
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      :  0.003   0.034   5934  Z= 0.145
  Angle     :  0.432   5.619   8014  Z= 0.254
  Chirality :  0.030   0.114    890
  Planarity :  0.002   0.024   1035
  Dihedral  :  9.646  68.563   2270
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  :  3.94 %
    Favored  : 93.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.00 (0.32), residues: 707
  helix:  3.81 (0.21), residues: 510
  sheet:  None (None), residues: 0
  loop : -0.75 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 139 
 TYR   0.009   0.001   TYR A 130 
 PHE   0.009   0.001   PHE D 145 
 TRP   0.008   0.001   TRP D 233 
 HIS   0.002   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5934)
  covalent geometry    : angle       0.43185 ( 8014)
  hydrogen bonds       : bond        0.11421 (  425)
  hydrogen bonds       : angle       4.65715 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 ASP cc_start: 0.7624 (m-30) cc_final: 0.7386 (t0)
REVERT: B  118 GLU cc_start: 0.7673 (pm20) cc_final: 0.7376 (pm20)
REVERT: B  216 TYR cc_start: 0.7034 (p90) cc_final: 0.6411 (t80)
REVERT: D  119 THR cc_start: 0.9279 (m) cc_final: 0.9020 (t)
  outliers start: 18
  outliers final: 10
  residues processed: 185
  average time/residue: 0.2117
  time to fit residues: 48.6258
Evaluate side-chains
  110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  135 ASP
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  167 GLU
Chi-restraints excluded: chain D residue  169 LYS
Chi-restraints excluded: chain D residue  230 GLN
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  332 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
A 166 GLN
B 116 GLN
B 229 ASN
D 130 HIS
D 211 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.105296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.088677 restraints weight = 48283.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.091682 restraints weight = 26984.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.093619 restraints weight = 17805.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.094955 restraints weight = 13177.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.095848 restraints weight = 10480.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5934  Z= 0.129
  Angle     :  0.490   5.140   8014  Z= 0.268
  Chirality :  0.031   0.119    890
  Planarity :  0.003   0.031   1035
  Dihedral  :  6.763  64.462    829
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 11.50 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.75 (0.31), residues: 707
  helix:  3.54 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -0.82 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  61 
 TYR   0.013   0.001   TYR B  49 
 PHE   0.009   0.001   PHE A 201 
 TRP   0.007   0.001   TRP D 233 
 HIS   0.005   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5934)
  covalent geometry    : angle       0.49037 ( 8014)
  hydrogen bonds       : bond        0.04202 (  425)
  hydrogen bonds       : angle       3.92800 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  216 TYR cc_start: 0.6916 (p90) cc_final: 0.6449 (t80)
  outliers start: 17
  outliers final: 9
  residues processed: 118
  average time/residue: 0.1726
  time to fit residues: 26.5044
Evaluate side-chains
  88 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain D residue  135 ASP
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  230 GLN
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 229 ASN
D 255 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.101516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.084503 restraints weight = 49339.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.087377 restraints weight = 28165.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.089174 restraints weight = 18907.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.090487 restraints weight = 14362.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.091371 restraints weight = 11607.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.4033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5934  Z= 0.226
  Angle     :  0.559   5.689   8014  Z= 0.314
  Chirality :  0.033   0.137    890
  Planarity :  0.004   0.031   1035
  Dihedral  :  6.057  65.914    818
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.39 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.81 (0.31), residues: 707
  helix:  2.81 (0.21), residues: 518
  sheet:  None (None), residues: 0
  loop : -0.99 (0.45), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 254 
 TYR   0.017   0.002   TYR A  49 
 PHE   0.012   0.002   PHE B 201 
 TRP   0.016   0.002   TRP B 233 
 HIS   0.007   0.002   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 5934)
  covalent geometry    : angle       0.55878 ( 8014)
  hydrogen bonds       : bond        0.04677 (  425)
  hydrogen bonds       : angle       4.29744 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  119 THR cc_start: 0.9250 (m) cc_final: 0.8909 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1867
  time to fit residues: 21.2174
Evaluate side-chains
  75 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain D residue  135 ASP
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  230 GLN
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  330 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.101336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.083989 restraints weight = 48598.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.087128 restraints weight = 25882.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.089165 restraints weight = 16755.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.090537 restraints weight = 12288.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.091491 restraints weight = 9781.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5934  Z= 0.152
  Angle     :  0.492   4.985   8014  Z= 0.272
  Chirality :  0.031   0.132    890
  Planarity :  0.004   0.030   1035
  Dihedral  :  5.971  65.769    818
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.91 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.98 (0.31), residues: 707
  helix:  2.96 (0.21), residues: 517
  sheet:  None (None), residues: 0
  loop : -0.98 (0.45), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 214 
 TYR   0.014   0.001   TYR B 130 
 PHE   0.009   0.001   PHE B 201 
 TRP   0.011   0.001   TRP D 233 
 HIS   0.006   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5934)
  covalent geometry    : angle       0.49189 ( 8014)
  hydrogen bonds       : bond        0.04253 (  425)
  hydrogen bonds       : angle       4.06908 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 PHE cc_start: 0.7713 (m-80) cc_final: 0.7486 (m-80)
REVERT: B  217 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6396 (pttm)
REVERT: D  271 TYR cc_start: 0.8559 (t80) cc_final: 0.8280 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 86
  average time/residue: 0.1763
  time to fit residues: 20.0205
Evaluate side-chains
  79 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain D residue  135 ASP
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  230 GLN
Chi-restraints excluded: chain D residue  311 ASP
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  330 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.9186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.100092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.083516 restraints weight = 48709.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.086271 restraints weight = 27478.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.088136 restraints weight = 18463.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.089381 restraints weight = 13802.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.090218 restraints weight = 11186.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5934  Z= 0.199
  Angle     :  0.519   4.581   8014  Z= 0.292
  Chirality :  0.032   0.129    890
  Planarity :  0.004   0.032   1035
  Dihedral  :  6.014  65.986    818
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.54 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.31), residues: 707
  helix:  2.70 (0.21), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.09 (0.44), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 279 
 TYR   0.016   0.002   TYR A  49 
 PHE   0.013   0.002   PHE B 201 
 TRP   0.010   0.001   TRP D 233 
 HIS   0.006   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 5934)
  covalent geometry    : angle       0.51896 ( 8014)
  hydrogen bonds       : bond        0.04466 (  425)
  hydrogen bonds       : angle       4.26723 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 PHE cc_start: 0.7706 (m-80) cc_final: 0.7485 (m-80)
REVERT: B  217 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6368 (pttm)
  outliers start: 17
  outliers final: 14
  residues processed: 79
  average time/residue: 0.1715
  time to fit residues: 17.9715
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain D residue  135 ASP
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  311 ASP
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  330 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 229 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.101642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.083802 restraints weight = 49214.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.087096 restraints weight = 25544.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.089237 restraints weight = 16283.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.090707 restraints weight = 11819.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.091700 restraints weight = 9311.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.4534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5934  Z= 0.119
  Angle     :  0.469   5.113   8014  Z= 0.255
  Chirality :  0.031   0.132    890
  Planarity :  0.003   0.028   1035
  Dihedral  :  5.300  45.388    815
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.49 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.01 (0.31), residues: 707
  helix:  2.97 (0.21), residues: 517
  sheet:  None (None), residues: 0
  loop : -0.94 (0.45), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 279 
 TYR   0.014   0.001   TYR A 184 
 PHE   0.010   0.001   PHE B 115 
 TRP   0.009   0.001   TRP D 233 
 HIS   0.006   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5934)
  covalent geometry    : angle       0.46893 ( 8014)
  hydrogen bonds       : bond        0.04039 (  425)
  hydrogen bonds       : angle       3.96227 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 PHE cc_start: 0.7777 (m-80) cc_final: 0.7568 (m-80)
REVERT: B  217 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6719 (pttm)
  outliers start: 14
  outliers final: 12
  residues processed: 78
  average time/residue: 0.1847
  time to fit residues: 18.8751
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain D residue  135 ASP
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  330 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    0.2980
   chunk 50 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 52 optimal weight:    0.2980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 229 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.103611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.087413 restraints weight = 48349.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.090297 restraints weight = 26723.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.092201 restraints weight = 17578.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.093502 restraints weight = 12919.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.094215 restraints weight = 10234.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.4568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5934  Z= 0.107
  Angle     :  0.449   4.705   8014  Z= 0.245
  Chirality :  0.031   0.126    890
  Planarity :  0.003   0.033   1035
  Dihedral  :  5.164  45.105    815
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.49 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.30 (0.32), residues: 707
  helix:  3.18 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -0.88 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 279 
 TYR   0.014   0.001   TYR A 184 
 PHE   0.008   0.001   PHE D 256 
 TRP   0.009   0.001   TRP D 233 
 HIS   0.006   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 5934)
  covalent geometry    : angle       0.44934 ( 8014)
  hydrogen bonds       : bond        0.03796 (  425)
  hydrogen bonds       : angle       3.82277 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6128 (pttm)
  outliers start: 11
  outliers final: 9
  residues processed: 82
  average time/residue: 0.1787
  time to fit residues: 19.3220
Evaluate side-chains
  77 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  311 ASP
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  330 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0470
   chunk 54 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.7078

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.103843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.087630 restraints weight = 47477.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.090571 restraints weight = 26105.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.092505 restraints weight = 17056.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.093787 restraints weight = 12474.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.094559 restraints weight = 9905.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.4729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5934  Z= 0.111
  Angle     :  0.458   5.493   8014  Z= 0.249
  Chirality :  0.031   0.143    890
  Planarity :  0.003   0.049   1035
  Dihedral  :  5.054  44.872    813
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.65 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.32 (0.32), residues: 707
  helix:  3.19 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -0.84 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 214 
 TYR   0.013   0.001   TYR A 184 
 PHE   0.007   0.001   PHE D 256 
 TRP   0.007   0.001   TRP B 233 
 HIS   0.005   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5934)
  covalent geometry    : angle       0.45783 ( 8014)
  hydrogen bonds       : bond        0.03762 (  425)
  hydrogen bonds       : angle       3.80992 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6051 (pttm)
  outliers start: 13
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1745
  time to fit residues: 17.8890
Evaluate side-chains
  77 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  330 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.099948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.081440 restraints weight = 49205.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.084605 restraints weight = 26758.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.086668 restraints weight = 17572.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.088091 restraints weight = 13036.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.089020 restraints weight = 10469.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.4918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5934  Z= 0.205
  Angle     :  0.533   5.156   8014  Z= 0.301
  Chirality :  0.032   0.137    890
  Planarity :  0.004   0.038   1035
  Dihedral  :  5.236  44.125    813
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.12 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.76 (0.31), residues: 707
  helix:  2.80 (0.21), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.05 (0.45), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 279 
 TYR   0.016   0.002   TYR B 130 
 PHE   0.014   0.002   PHE D 256 
 TRP   0.008   0.001   TRP A  60 
 HIS   0.006   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 5934)
  covalent geometry    : angle       0.53309 ( 8014)
  hydrogen bonds       : bond        0.04328 (  425)
  hydrogen bonds       : angle       4.19013 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6977 (pttm)
  outliers start: 12
  outliers final: 11
  residues processed: 70
  average time/residue: 0.1870
  time to fit residues: 17.0905
Evaluate side-chains
  72 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  311 ASP
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  330 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0970
   chunk 41 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.103315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.086995 restraints weight = 47979.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.089905 restraints weight = 26367.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.091838 restraints weight = 17232.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.093100 restraints weight = 12614.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.093938 restraints weight = 10057.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.4878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5934  Z= 0.112
  Angle     :  0.471   5.486   8014  Z= 0.258
  Chirality :  0.031   0.129    890
  Planarity :  0.004   0.039   1035
  Dihedral  :  5.126  43.022    813
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.59 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.26 (0.32), residues: 707
  helix:  3.15 (0.21), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.70 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 279 
 TYR   0.010   0.001   TYR B 130 
 PHE   0.015   0.001   PHE B 115 
 TRP   0.009   0.001   TRP B 233 
 HIS   0.006   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 5934)
  covalent geometry    : angle       0.47100 ( 8014)
  hydrogen bonds       : bond        0.03910 (  425)
  hydrogen bonds       : angle       3.87238 ( 1260)

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

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

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1414 Ramachandran restraints generated.
    707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6540 (pttm)
  outliers start: 11
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1848
  time to fit residues: 17.5185
Evaluate side-chains
  74 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain D residue  140 MET
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  311 ASP
Chi-restraints excluded: chain D residue  318 ARG
Chi-restraints excluded: chain D residue  322 LYS
Chi-restraints excluded: chain D residue  330 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.102248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.085807 restraints weight = 48035.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.088669 restraints weight = 26680.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.090557 restraints weight = 17580.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.091822 restraints weight = 12989.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.092697 restraints weight = 10399.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5934  Z= 0.150
  Angle     :  0.516   9.451   8014  Z= 0.283
  Chirality :  0.032   0.213    890
  Planarity :  0.004   0.044   1035
  Dihedral  :  5.126  42.508    813
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.38 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.75 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.14 (0.31), residues: 707
  helix:  3.06 (0.21), residues: 510
  sheet:  None (None), residues: 0
  loop : -0.73 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 279 
 TYR   0.013   0.001   TYR B 130 
 PHE   0.010   0.001   PHE D 256 
 TRP   0.006   0.001   TRP D 212 
 HIS   0.005   0.001   HIS D 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5934)
  covalent geometry    : angle       0.51628 ( 8014)
  hydrogen bonds       : bond        0.04021 (  425)
  hydrogen bonds       : angle       4.01158 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2101.31 seconds
wall clock time: 36 minutes 30.87 seconds (2190.87 seconds total)