Starting phenix.real_space_refine
on Tue Feb  3 20:24:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u82_63950/02_2026/9u82_63950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u82_63950/02_2026/9u82_63950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u82_63950/02_2026/9u82_63950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u82_63950/02_2026/9u82_63950.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u82_63950/02_2026/9u82_63950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u82_63950/02_2026/9u82_63950.map"
  }
  resolution = 2.7
  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=   0.002 sd=   0.007
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      36      5.16       5
     C    4422      2.51       5
     N    1098      2.21       5
     O    1152      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6708
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3354
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3354
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 19, 'TRANS': 428}
    Chain: "B"
      Number of atoms: 3354
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3354
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 19, 'TRANS': 428}
  Time building chain proxies: 1.21, per 1000 atoms: 0.18
  Number of scatterers: 6708
  At special positions: 0
  Unit cell: (75.952, 74.448, 106.784, 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      36     16.00
     O    1152      8.00
     N    1098      7.00
     C    4422      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 263.1 milliseconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1608

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 4 sheets defined
      82.5% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 29
      removed outlier: 3.526A  pdb=" N   ILE A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A  13 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      Proline residue:  A  14  - end of helix
      removed outlier: 3.717A  pdb=" N   LEU A  18 " --> pdb=" O   PRO A  14 " (cutoff:3.500A)
      Proline residue:  A  19  - end of helix
    Processing helix  chain 'A' and resid 32 through 72
      removed outlier: 3.588A  pdb=" N   GLY A  62 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      Proline residue:  A  63  - end of helix
    Processing helix  chain 'A' and resid 81 through 92
      removed outlier: 3.523A  pdb=" N   GLY A  85 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 95 through 113
      removed outlier: 4.192A  pdb=" N   ILE A 100 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
      Proline residue:  A 101  - end of helix
    Processing helix  chain 'A' and resid 122 through 125
    Processing helix  chain 'A' and resid 126 through 141
    Processing helix  chain 'A' and resid 142 through 164
    Processing helix  chain 'A' and resid 164 through 171
    Processing helix  chain 'A' and resid 181 through 201
      removed outlier: 3.926A  pdb=" N   ALA A 185 " --> pdb=" O   HIS A 181 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TYR A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 210 through 219
    Processing helix  chain 'A' and resid 220 through 222
      No H-bonds generated for 'chain 'A' and resid 220 through 222'
    Processing helix  chain 'A' and resid 223 through 239
    Processing helix  chain 'A' and resid 242 through 287
      Proline residue:  A 261  - end of helix
      Proline residue:  A 266  - end of helix
      Proline residue:  A 273  - end of helix
      removed outlier: 4.512A  pdb=" N   GLN A 283 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ALA A 284 " --> pdb=" O   SER A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 303 through 324
      removed outlier: 3.822A  pdb=" N   ILE A 314 " --> pdb=" O   SER A 310 " (cutoff:3.500A)
      Proline residue:  A 315  - end of helix
    Processing helix  chain 'A' and resid 337 through 341
    Processing helix  chain 'A' and resid 342 through 349
      removed outlier: 3.637A  pdb=" N   ALA A 347 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 374
    Processing helix  chain 'A' and resid 374 through 385
    Processing helix  chain 'A' and resid 403 through 415
    Processing helix  chain 'A' and resid 417 through 448
    Processing helix  chain 'B' and resid 2 through 29
      Proline residue:  B  14  - end of helix
      removed outlier: 3.705A  pdb=" N   LEU B  18 " --> pdb=" O   PRO B  14 " (cutoff:3.500A)
      Proline residue:  B  19  - end of helix
    Processing helix  chain 'B' and resid 32 through 72
      removed outlier: 3.708A  pdb=" N   GLY B  62 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      Proline residue:  B  63  - end of helix
    Processing helix  chain 'B' and resid 82 through 92
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 95 through 113
      removed outlier: 4.208A  pdb=" N   ILE B 100 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      Proline residue:  B 101  - end of helix
    Processing helix  chain 'B' and resid 122 through 125
    Processing helix  chain 'B' and resid 126 through 141
    Processing helix  chain 'B' and resid 142 through 164
    Processing helix  chain 'B' and resid 164 through 171
    Processing helix  chain 'B' and resid 181 through 201
      removed outlier: 3.889A  pdb=" N   ALA B 185 " --> pdb=" O   HIS B 181 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   TYR B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
      Proline residue:  B 189  - end of helix
    Processing helix  chain 'B' and resid 210 through 219
    Processing helix  chain 'B' and resid 220 through 222
      No H-bonds generated for 'chain 'B' and resid 220 through 222'
    Processing helix  chain 'B' and resid 223 through 239
    Processing helix  chain 'B' and resid 242 through 287
      Proline residue:  B 261  - end of helix
      Proline residue:  B 266  - end of helix
      Proline residue:  B 273  - end of helix
      removed outlier: 4.506A  pdb=" N   GLN B 283 " --> pdb=" O   ARG B 279 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ALA B 284 " --> pdb=" O   SER B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 302
    Processing helix  chain 'B' and resid 303 through 324
      removed outlier: 3.780A  pdb=" N   ILE B 314 " --> pdb=" O   SER B 310 " (cutoff:3.500A)
      Proline residue:  B 315  - end of helix
    Processing helix  chain 'B' and resid 338 through 349
      removed outlier: 4.037A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   MET B 344 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   ALA B 345 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA B 347 " --> pdb=" O   ALA B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 374
    Processing helix  chain 'B' and resid 374 through 385
    Processing helix  chain 'B' and resid 403 through 415
    Processing helix  chain 'B' and resid 417 through 448
    Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 79
      removed outlier: 6.823A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 78 through 79
      removed outlier: 6.884A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 120

    504 hydrogen bonds defined for protein.
    1476 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: 1.11

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2096
        1.34 -     1.46: 1522
        1.46 -     1.58: 3160
        1.58 -     1.70: 0
        1.70 -     1.81: 72
  Bond restraints: 6850
  Sorted by residual:
  bond pdb=" CA  ALA A 220 "
       pdb=" C   ALA A 220 "
    ideal  model  delta    sigma   weight residual
    1.522  1.508  0.014 1.38e-02 5.25e+03 1.05e+00
  bond pdb=" CB  THR A  90 "
       pdb=" CG2 THR A  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 9.06e-01
  bond pdb=" CB  PRO A  19 "
       pdb=" CG  PRO A  19 "
    ideal  model  delta    sigma   weight residual
    1.492  1.447  0.045 5.00e-02 4.00e+02 8.09e-01
  bond pdb=" CB  ILE A  61 "
       pdb=" CG2 ILE A  61 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.14e-01
  bond pdb=" CB  THR B  90 "
       pdb=" CG2 THR B  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.03e-01
  ... (remaining 6845 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 9226
        2.23 -     4.45: 82
        4.45 -     6.68: 20
        6.68 -     8.90: 3
        8.90 -    11.13: 1
  Bond angle restraints: 9332
  Sorted by residual:
  angle pdb=" CB  MET A 364 "
        pdb=" CG  MET A 364 "
        pdb=" SD  MET A 364 "
      ideal   model   delta    sigma   weight residual
     112.70  123.83  -11.13 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" N   ILE B 126 "
        pdb=" CA  ILE B 126 "
        pdb=" C   ILE B 126 "
      ideal   model   delta    sigma   weight residual
     113.00  108.37    4.63 1.30e+00 5.92e-01 1.27e+01
  angle pdb=" CA  GLU A   4 "
        pdb=" CB  GLU A   4 "
        pdb=" CG  GLU A   4 "
      ideal   model   delta    sigma   weight residual
     114.10  119.36   -5.26 2.00e+00 2.50e-01 6.91e+00
  angle pdb=" CB  MET B 260 "
        pdb=" CG  MET B 260 "
        pdb=" SD  MET B 260 "
      ideal   model   delta    sigma   weight residual
     112.70  120.45   -7.75 3.00e+00 1.11e-01 6.67e+00
  angle pdb=" CB  MET B 231 "
        pdb=" CG  MET B 231 "
        pdb=" SD  MET B 231 "
      ideal   model   delta    sigma   weight residual
     112.70  120.38   -7.68 3.00e+00 1.11e-01 6.56e+00
  ... (remaining 9327 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.25: 3479
       14.25 -    28.50: 338
       28.50 -    42.74: 110
       42.74 -    56.99: 59
       56.99 -    71.24: 12
  Dihedral angle restraints: 3998
    sinusoidal: 1482
      harmonic: 2516
  Sorted by residual:
  dihedral pdb=" CA  LEU B 357 "
           pdb=" CB  LEU B 357 "
           pdb=" CG  LEU B 357 "
           pdb=" CD1 LEU B 357 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.20   59.80     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET A 398 "
           pdb=" CG  MET A 398 "
           pdb=" SD  MET A 398 "
           pdb=" CE  MET A 398 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -2.48  -57.52     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CA  LEU A 292 "
           pdb=" CB  LEU A 292 "
           pdb=" CG  LEU A 292 "
           pdb=" CD1 LEU A 292 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.61  -56.61     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 3995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 630
       0.028 -    0.057: 320
       0.057 -    0.085: 135
       0.085 -    0.113: 49
       0.113 -    0.142: 18
  Chirality restraints: 1152
  Sorted by residual:
  chirality pdb=" CA  SER B  87 "
            pdb=" N   SER B  87 "
            pdb=" C   SER B  87 "
            pdb=" CB  SER B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  SER A  87 "
            pdb=" N   SER A  87 "
            pdb=" C   SER A  87 "
            pdb=" CB  SER A  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  PRO A 101 "
            pdb=" N   PRO A 101 "
            pdb=" C   PRO A 101 "
            pdb=" CB  PRO A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 1149 not shown)

  Planarity restraints: 1146
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 188 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO B 189 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 189 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 189 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 188 "    0.027 5.00e-02 4.00e+02   4.03e-02 2.59e+00
        pdb=" N   PRO A 189 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  18 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO B  19 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B  19 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  19 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1143 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 66
        2.67 -     3.23: 6798
        3.23 -     3.78: 11663
        3.78 -     4.34: 15089
        4.34 -     4.90: 25405
  Nonbonded interactions: 59021
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 186 "
            pdb=" OH  TYR B 428 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" O   TYR A 186 "
            pdb=" OH  TYR A 428 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" O   VAL A 410 "
            pdb=" OG1 THR A 414 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" N   GLU A   4 "
            pdb=" OE1 GLU A   4 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OG1 THR A 389 "
            pdb=" OD1 ASP A 391 "
     model   vdw
     2.262 3.040
  ... (remaining 59016 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.080
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
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      :  0.006   0.045   6850  Z= 0.231
  Angle     :  0.589  11.130   9332  Z= 0.293
  Chirality :  0.043   0.142   1152
  Planarity :  0.004   0.041   1146
  Dihedral  : 14.839  71.237   2390
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 15.72 %
    Favored  : 83.29 %
  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:  2.48 (0.27), residues: 892
  helix:  2.22 (0.19), residues: 678
  sheet:  None (None), residues: 0
  loop : -0.22 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 438 
 TYR   0.021   0.002   TYR A 186 
 PHE   0.014   0.002   PHE A 313 
 TRP   0.022   0.002   TRP B 124 
 HIS   0.002   0.001   HIS B 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 6850)
  covalent geometry    : angle       0.58933 ( 9332)
  hydrogen bonds       : bond        0.10498 (  504)
  hydrogen bonds       : angle       4.91526 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6921 (tpp) cc_final: 0.5575 (pp-130)
REVERT: B  199 GLU cc_start: 0.9147 (tp30) cc_final: 0.8891 (tp30)
REVERT: B  223 GLU cc_start: 0.7593 (tp30) cc_final: 0.7371 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 58
  average time/residue: 0.6628
  time to fit residues: 40.2260
Evaluate side-chains
  57 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  225 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 208 HIS
A 400 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.071153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.055534 restraints weight = 16891.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.81
r_work: 0.2877 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.0637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6850  Z= 0.131
  Angle     :  0.512   7.943   9332  Z= 0.259
  Chirality :  0.041   0.135   1152
  Planarity :  0.004   0.039   1146
  Dihedral  :  4.470  52.746    940
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 13.46 %
    Favored  : 83.57 %
  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:  2.67 (0.28), residues: 892
  helix:  2.27 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop : -0.13 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 355 
 TYR   0.017   0.001   TYR B 158 
 PHE   0.009   0.001   PHE A   2 
 TRP   0.014   0.001   TRP B 124 
 HIS   0.004   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6850)
  covalent geometry    : angle       0.51225 ( 9332)
  hydrogen bonds       : bond        0.03864 (  504)
  hydrogen bonds       : angle       4.24426 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6768 (tpp) cc_final: 0.5594 (pp-130)
REVERT: A  199 GLU cc_start: 0.9019 (tp30) cc_final: 0.8676 (mm-30)
REVERT: B  199 GLU cc_start: 0.9140 (tp30) cc_final: 0.8919 (tp30)
REVERT: B  364 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7070 (mpp)
REVERT: B  416 GLU cc_start: 0.8851 (tt0) cc_final: 0.8633 (pt0)
  outliers start: 21
  outliers final: 5
  residues processed: 71
  average time/residue: 0.5652
  time to fit residues: 42.3060
Evaluate side-chains
  63 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 MET
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.055939 restraints weight = 16742.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.81
r_work: 0.2897 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.0891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6850  Z= 0.123
  Angle     :  0.495   6.755   9332  Z= 0.249
  Chirality :  0.040   0.135   1152
  Planarity :  0.003   0.040   1146
  Dihedral  :  3.730  26.391    935
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.74 %
    Favored  : 83.57 %
  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:  2.78 (0.28), residues: 892
  helix:  2.37 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.09 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 355 
 TYR   0.018   0.001   TYR B 158 
 PHE   0.015   0.001   PHE A   2 
 TRP   0.014   0.001   TRP B 124 
 HIS   0.002   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6850)
  covalent geometry    : angle       0.49463 ( 9332)
  hydrogen bonds       : bond        0.03636 (  504)
  hydrogen bonds       : angle       4.07304 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A    3 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8747 (t)
REVERT: A  199 GLU cc_start: 0.9015 (tp30) cc_final: 0.8661 (mm-30)
REVERT: A  416 GLU cc_start: 0.8737 (pt0) cc_final: 0.8457 (pp20)
REVERT: B    1 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6746 (tpt)
REVERT: B  199 GLU cc_start: 0.9138 (tp30) cc_final: 0.8912 (tp30)
REVERT: B  223 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7331 (mp0)
REVERT: B  416 GLU cc_start: 0.8883 (tt0) cc_final: 0.8668 (pt0)
  outliers start: 19
  outliers final: 2
  residues processed: 70
  average time/residue: 0.5882
  time to fit residues: 43.2689
Evaluate side-chains
  61 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 47 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 42 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.071442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.055856 restraints weight = 16828.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.84
r_work: 0.2891 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.0912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6850  Z= 0.128
  Angle     :  0.498   7.482   9332  Z= 0.250
  Chirality :  0.040   0.134   1152
  Planarity :  0.003   0.040   1146
  Dihedral  :  3.603  15.209    934
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.16 %
    Favored  : 83.57 %
  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 (0.28), residues: 892
  helix:  2.39 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.09 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 355 
 TYR   0.017   0.001   TYR B 158 
 PHE   0.013   0.001   PHE A   2 
 TRP   0.014   0.001   TRP B 124 
 HIS   0.002   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6850)
  covalent geometry    : angle       0.49828 ( 9332)
  hydrogen bonds       : bond        0.03540 (  504)
  hydrogen bonds       : angle       4.01020 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A    3 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8807 (t)
REVERT: A  199 GLU cc_start: 0.9019 (tp30) cc_final: 0.8702 (mm-30)
REVERT: A  416 GLU cc_start: 0.8700 (pt0) cc_final: 0.8403 (pp20)
REVERT: B  199 GLU cc_start: 0.9147 (tp30) cc_final: 0.8937 (tp30)
REVERT: B  223 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7413 (mp0)
REVERT: B  416 GLU cc_start: 0.8839 (tt0) cc_final: 0.8627 (pt0)
  outliers start: 16
  outliers final: 5
  residues processed: 70
  average time/residue: 0.5927
  time to fit residues: 43.5350
Evaluate side-chains
  64 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.072103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.056526 restraints weight = 17012.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.85
r_work: 0.2908 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6850  Z= 0.111
  Angle     :  0.485   5.932   9332  Z= 0.243
  Chirality :  0.040   0.132   1152
  Planarity :  0.003   0.039   1146
  Dihedral  :  3.561  15.072    934
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.02 %
    Favored  : 83.43 %
  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:  2.86 (0.28), residues: 892
  helix:  2.43 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.05 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 355 
 TYR   0.019   0.001   TYR B 158 
 PHE   0.009   0.001   PHE A   2 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6850)
  covalent geometry    : angle       0.48523 ( 9332)
  hydrogen bonds       : bond        0.03393 (  504)
  hydrogen bonds       : angle       3.93665 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A    3 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8791 (t)
REVERT: A  199 GLU cc_start: 0.9014 (tp30) cc_final: 0.8770 (mm-30)
REVERT: A  416 GLU cc_start: 0.8689 (pt0) cc_final: 0.8441 (pp20)
REVERT: B  199 GLU cc_start: 0.9140 (tp30) cc_final: 0.8927 (tp30)
REVERT: B  223 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7379 (mp0)
REVERT: B  364 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8357 (mmt)
REVERT: B  395 VAL cc_start: 0.8121 (t) cc_final: 0.7687 (p)
REVERT: B  416 GLU cc_start: 0.8838 (tt0) cc_final: 0.8632 (pt0)
  outliers start: 18
  outliers final: 5
  residues processed: 74
  average time/residue: 0.5961
  time to fit residues: 46.4160
Evaluate side-chains
  65 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0030
   chunk 17 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0980
   chunk 30 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    0.7992

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.072452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.056887 restraints weight = 16862.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.84
r_work: 0.2921 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6850  Z= 0.109
  Angle     :  0.494   6.630   9332  Z= 0.246
  Chirality :  0.040   0.133   1152
  Planarity :  0.003   0.039   1146
  Dihedral  :  3.546  14.874    934
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 13.88 %
    Favored  : 83.00 %
  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:  2.90 (0.28), residues: 892
  helix:  2.45 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.04 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 355 
 TYR   0.021   0.001   TYR B 158 
 PHE   0.011   0.001   PHE A   2 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6850)
  covalent geometry    : angle       0.49378 ( 9332)
  hydrogen bonds       : bond        0.03366 (  504)
  hydrogen bonds       : angle       3.89570 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6559 (tpp) cc_final: 0.5414 (pp-130)
REVERT: A  199 GLU cc_start: 0.9041 (tp30) cc_final: 0.8818 (mm-30)
REVERT: A  282 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8516 (tm)
REVERT: B  199 GLU cc_start: 0.9149 (tp30) cc_final: 0.8939 (tp30)
REVERT: B  223 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7408 (mp0)
REVERT: B  364 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8373 (mmt)
REVERT: B  395 VAL cc_start: 0.8146 (t) cc_final: 0.7714 (p)
REVERT: B  416 GLU cc_start: 0.8835 (tt0) cc_final: 0.8619 (pt0)
  outliers start: 22
  outliers final: 7
  residues processed: 77
  average time/residue: 0.5778
  time to fit residues: 46.8611
Evaluate side-chains
  69 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  364 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.072240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.056726 restraints weight = 16752.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.83
r_work: 0.2916 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6850  Z= 0.117
  Angle     :  0.509   6.827   9332  Z= 0.252
  Chirality :  0.040   0.138   1152
  Planarity :  0.003   0.039   1146
  Dihedral  :  3.510  14.787    934
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.02 %
    Favored  : 83.43 %
  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:  2.92 (0.28), residues: 892
  helix:  2.49 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.09 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 355 
 TYR   0.019   0.001   TYR B 158 
 PHE   0.010   0.001   PHE A  47 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6850)
  covalent geometry    : angle       0.50913 ( 9332)
  hydrogen bonds       : bond        0.03363 (  504)
  hydrogen bonds       : angle       3.88709 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6528 (tpp) cc_final: 0.5471 (pp-130)
REVERT: A  199 GLU cc_start: 0.9019 (tp30) cc_final: 0.8802 (mm-30)
REVERT: B  199 GLU cc_start: 0.9142 (tp30) cc_final: 0.8928 (tp30)
REVERT: B  223 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7375 (mp0)
REVERT: B  364 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8338 (mmt)
REVERT: B  395 VAL cc_start: 0.8133 (t) cc_final: 0.7696 (p)
REVERT: B  416 GLU cc_start: 0.8825 (tt0) cc_final: 0.8617 (pt0)
  outliers start: 18
  outliers final: 9
  residues processed: 73
  average time/residue: 0.6402
  time to fit residues: 49.1094
Evaluate side-chains
  68 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  364 MET
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.055354 restraints weight = 16944.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.85
r_work: 0.2881 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6850  Z= 0.162
  Angle     :  0.552   9.248   9332  Z= 0.270
  Chirality :  0.041   0.153   1152
  Planarity :  0.003   0.040   1146
  Dihedral  :  3.551  14.952    934
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 14.73 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.28), residues: 892
  helix:  2.40 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.12 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A   7 
 TYR   0.020   0.002   TYR B 158 
 PHE   0.010   0.001   PHE A  47 
 TRP   0.015   0.001   TRP B 124 
 HIS   0.002   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6850)
  covalent geometry    : angle       0.55245 ( 9332)
  hydrogen bonds       : bond        0.03562 (  504)
  hydrogen bonds       : angle       3.96850 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6573 (tpp) cc_final: 0.5392 (pp-130)
REVERT: A  199 GLU cc_start: 0.9032 (tp30) cc_final: 0.8740 (mm-30)
REVERT: B  199 GLU cc_start: 0.9142 (tp30) cc_final: 0.8923 (tp30)
REVERT: B  223 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7388 (mp0)
REVERT: B  416 GLU cc_start: 0.8847 (tt0) cc_final: 0.8639 (pt0)
  outliers start: 17
  outliers final: 7
  residues processed: 70
  average time/residue: 0.6588
  time to fit residues: 48.4168
Evaluate side-chains
  66 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 10 optimal weight:    0.0370
   chunk 22 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.073298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.057089 restraints weight = 16721.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 3.00
r_work: 0.2904 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6850  Z= 0.114
  Angle     :  0.537   8.105   9332  Z= 0.264
  Chirality :  0.040   0.139   1152
  Planarity :  0.003   0.039   1146
  Dihedral  :  3.553  15.073    934
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.44 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.89 (0.28), residues: 892
  helix:  2.46 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.07 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 117 
 TYR   0.025   0.001   TYR B 158 
 PHE   0.010   0.001   PHE A  47 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6850)
  covalent geometry    : angle       0.53698 ( 9332)
  hydrogen bonds       : bond        0.03352 (  504)
  hydrogen bonds       : angle       3.88563 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6494 (tpp) cc_final: 0.5314 (pp-130)
REVERT: A  199 GLU cc_start: 0.9027 (tp30) cc_final: 0.8770 (mm-30)
REVERT: B  199 GLU cc_start: 0.9138 (tp30) cc_final: 0.8911 (tp30)
REVERT: B  223 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7316 (mp0)
REVERT: B  395 VAL cc_start: 0.7982 (t) cc_final: 0.7539 (p)
REVERT: B  416 GLU cc_start: 0.8841 (tt0) cc_final: 0.8635 (pt0)
  outliers start: 12
  outliers final: 6
  residues processed: 69
  average time/residue: 0.6724
  time to fit residues: 48.6915
Evaluate side-chains
  65 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  353 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 72 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.072180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.056478 restraints weight = 16871.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.85
r_work: 0.2911 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6850  Z= 0.124
  Angle     :  0.546   9.957   9332  Z= 0.267
  Chirality :  0.040   0.137   1152
  Planarity :  0.003   0.039   1146
  Dihedral  :  3.539  14.952    934
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 15.58 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.87 (0.28), residues: 892
  helix:  2.44 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.08 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 114 
 TYR   0.024   0.001   TYR B 158 
 PHE   0.012   0.001   PHE A   2 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6850)
  covalent geometry    : angle       0.54634 ( 9332)
  hydrogen bonds       : bond        0.03389 (  504)
  hydrogen bonds       : angle       3.88655 ( 1476)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6354 (tpp) cc_final: 0.5140 (pp-130)
REVERT: A  199 GLU cc_start: 0.9041 (tp30) cc_final: 0.8806 (mm-30)
REVERT: B  199 GLU cc_start: 0.9148 (tp30) cc_final: 0.8935 (tp30)
REVERT: B  223 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7419 (mp0)
REVERT: B  364 MET cc_start: 0.8650 (mpp) cc_final: 0.8412 (mmt)
REVERT: B  395 VAL cc_start: 0.8172 (t) cc_final: 0.7739 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 67
  average time/residue: 0.6785
  time to fit residues: 47.5682
Evaluate side-chains
  67 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  223 GLU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.072905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.057069 restraints weight = 17002.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.89
r_work: 0.2928 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6850  Z= 0.116
  Angle     :  0.543  10.000   9332  Z= 0.265
  Chirality :  0.040   0.140   1152
  Planarity :  0.003   0.039   1146
  Dihedral  :  3.523  14.872    934
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.30 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.90 (0.28), residues: 892
  helix:  2.46 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.05 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 355 
 TYR   0.024   0.001   TYR B 158 
 PHE   0.010   0.001   PHE A  47 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6850)
  covalent geometry    : angle       0.54269 ( 9332)
  hydrogen bonds       : bond        0.03326 (  504)
  hydrogen bonds       : angle       3.84055 ( 1476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1786.81 seconds
wall clock time: 31 minutes 27.32 seconds (1887.32 seconds total)