Starting phenix.real_space_refine
on Sun Apr  5 00:32:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10tp_75462/04_2026/10tp_75462_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10tp_75462/04_2026/10tp_75462.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/10tp_75462/04_2026/10tp_75462.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10tp_75462/04_2026/10tp_75462.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/10tp_75462/04_2026/10tp_75462_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10tp_75462/04_2026/10tp_75462_neut.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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      20      5.16       5
     C    4266      2.51       5
     N    1046      2.21       5
     O    1070      1.98       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: 6402
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3201
          Classifications: {'peptide': 428}
          Link IDs: {'PTRANS': 15, 'TRANS': 412}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.01, per 1000 atoms: 0.31
  Number of scatterers: 6402
  At special positions: 0
  Unit cell: (66.95, 113.75, 74.1, 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      20     16.00
     O    1070      8.00
     N    1046      7.00
     C    4266      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: 0.63
  Conformation dependent library (CDL) restraints added in 180.0 milliseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1564

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      90.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 18
    Processing helix  chain 'A' and resid 19 through 22
    Processing helix  chain 'A' and resid 23 through 38
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 73
      removed outlier: 5.258A  pdb=" N   ASN A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   ALA A  56 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   THR A  59 " --> pdb=" O   ASN A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 86
    Processing helix  chain 'A' and resid 90 through 110
      removed outlier: 4.316A  pdb=" N   LEU A 108 " --> pdb=" O   SER A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
    Processing helix  chain 'A' and resid 117 through 130
      removed outlier: 3.880A  pdb=" N   ILE A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 150
      removed outlier: 4.357A  pdb=" N   ASP A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 157
    Processing helix  chain 'A' and resid 158 through 168
    Processing helix  chain 'A' and resid 171 through 198
      Proline residue:  A 181  - end of helix
    Processing helix  chain 'A' and resid 207 through 211
      removed outlier: 3.634A  pdb=" N   GLN A 210 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 218
    Processing helix  chain 'A' and resid 220 through 241
    Processing helix  chain 'A' and resid 247 through 267
      removed outlier: 3.633A  pdb=" N   VAL A 251 " --> pdb=" O   PRO A 247 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   HIS A 267 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 280 through 299
      removed outlier: 4.115A  pdb=" N   VAL A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TYR A 290 " --> pdb=" O   SER A 286 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LEU A 291 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ARG A 297 " --> pdb=" O   VAL A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 314
      removed outlier: 3.765A  pdb=" N   HIS A 304 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 308 " --> pdb=" O   HIS A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 336
    Processing helix  chain 'A' and resid 337 through 350
      removed outlier: 3.984A  pdb=" N   LEU A 342 " --> pdb=" O   MET A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 372
    Processing helix  chain 'A' and resid 376 through 379
    Processing helix  chain 'A' and resid 380 through 393
    Processing helix  chain 'A' and resid 398 through 427
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'B' and resid 2 through 18
    Processing helix  chain 'B' and resid 19 through 22
    Processing helix  chain 'B' and resid 23 through 38
    Processing helix  chain 'B' and resid 42 through 44
      No H-bonds generated for 'chain 'B' and resid 42 through 44'
    Processing helix  chain 'B' and resid 45 through 73
      removed outlier: 5.258A  pdb=" N   ASN B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   ALA B  56 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   THR B  59 " --> pdb=" O   ASN B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 86
    Processing helix  chain 'B' and resid 90 through 110
      removed outlier: 4.317A  pdb=" N   LEU B 108 " --> pdb=" O   SER B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 116
    Processing helix  chain 'B' and resid 117 through 130
      removed outlier: 3.880A  pdb=" N   ILE B 121 " --> pdb=" O   ILE B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 150
      removed outlier: 4.356A  pdb=" N   ASP B 148 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 157
    Processing helix  chain 'B' and resid 158 through 168
    Processing helix  chain 'B' and resid 171 through 198
      Proline residue:  B 181  - end of helix
    Processing helix  chain 'B' and resid 207 through 211
      removed outlier: 3.635A  pdb=" N   GLN B 210 " --> pdb=" O   ASP B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 218
    Processing helix  chain 'B' and resid 220 through 241
    Processing helix  chain 'B' and resid 247 through 267
      removed outlier: 3.633A  pdb=" N   VAL B 251 " --> pdb=" O   PRO B 247 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   HIS B 267 " --> pdb=" O   ALA B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 278
    Processing helix  chain 'B' and resid 280 through 299
      removed outlier: 4.116A  pdb=" N   VAL B 284 " --> pdb=" O   TRP B 280 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TYR B 290 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU B 291 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU B 296 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ARG B 297 " --> pdb=" O   VAL B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 314
      removed outlier: 3.765A  pdb=" N   HIS B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU B 308 " --> pdb=" O   HIS B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 336
    Processing helix  chain 'B' and resid 337 through 350
      removed outlier: 3.984A  pdb=" N   LEU B 342 " --> pdb=" O   MET B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 372
    Processing helix  chain 'B' and resid 376 through 379
    Processing helix  chain 'B' and resid 380 through 393
    Processing helix  chain 'B' and resid 398 through 427
      Proline residue:  B 412  - end of helix

    529 hydrogen bonds defined for protein.
    1545 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: 1.13

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1927
        1.34 -     1.45: 868
        1.45 -     1.57: 3713
        1.57 -     1.68: 0
        1.68 -     1.80: 40
  Bond restraints: 6548
  Sorted by residual:
  bond pdb=" N   ILE A  61 "
       pdb=" CA  ILE A  61 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.19e-02 7.06e+03 6.53e+00
  bond pdb=" N   ILE B  61 "
       pdb=" CA  ILE B  61 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.19e-02 7.06e+03 6.52e+00
  bond pdb=" N   THR A  59 "
       pdb=" CA  THR A  59 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.59e+00
  bond pdb=" N   THR B  59 "
       pdb=" CA  THR B  59 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.58e+00
  bond pdb=" N   PHE B  60 "
       pdb=" CA  PHE B  60 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.026 1.19e-02 7.06e+03 4.87e+00
  ... (remaining 6543 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 8375
        1.23 -     2.47: 488
        2.47 -     3.70: 71
        3.70 -     4.94: 20
        4.94 -     6.17: 12
  Bond angle restraints: 8966
  Sorted by residual:
  angle pdb=" CA  ILE A  61 "
        pdb=" C   ILE A  61 "
        pdb=" O   ILE A  61 "
      ideal   model   delta    sigma   weight residual
     120.95  117.72    3.23 1.04e+00 9.25e-01 9.66e+00
  angle pdb=" CA  ILE B  61 "
        pdb=" C   ILE B  61 "
        pdb=" O   ILE B  61 "
      ideal   model   delta    sigma   weight residual
     120.95  117.77    3.18 1.04e+00 9.25e-01 9.33e+00
  angle pdb=" CA  THR B  59 "
        pdb=" C   THR B  59 "
        pdb=" O   THR B  59 "
      ideal   model   delta    sigma   weight residual
     120.55  117.93    2.62 1.06e+00 8.90e-01 6.13e+00
  angle pdb=" N   ILE A  61 "
        pdb=" CA  ILE A  61 "
        pdb=" C   ILE A  61 "
      ideal   model   delta    sigma   weight residual
     110.62  108.10    2.52 1.02e+00 9.61e-01 6.09e+00
  angle pdb=" N   ILE B  61 "
        pdb=" CA  ILE B  61 "
        pdb=" C   ILE B  61 "
      ideal   model   delta    sigma   weight residual
     110.62  108.13    2.49 1.02e+00 9.61e-01 5.96e+00
  ... (remaining 8961 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.63: 3310
       10.63 -    21.26: 318
       21.26 -    31.88: 98
       31.88 -    42.51: 28
       42.51 -    53.14: 6
  Dihedral angle restraints: 3760
    sinusoidal: 1324
      harmonic: 2436
  Sorted by residual:
  dihedral pdb=" CA  LEU B 152 "
           pdb=" C   LEU B 152 "
           pdb=" N   PRO B 153 "
           pdb=" CA  PRO B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.00  -27.00     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  LEU A 152 "
           pdb=" C   LEU A 152 "
           pdb=" N   PRO A 153 "
           pdb=" CA  PRO A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.01  -26.99     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  ASP B 220 "
           pdb=" C   ASP B 220 "
           pdb=" N   VAL B 221 "
           pdb=" CA  VAL B 221 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.47  -17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 3757 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 624
       0.031 -    0.062: 338
       0.062 -    0.093: 127
       0.093 -    0.124: 32
       0.124 -    0.156: 7
  Chirality restraints: 1128
  Sorted by residual:
  chirality pdb=" CA  PRO B 153 "
            pdb=" N   PRO B 153 "
            pdb=" C   PRO B 153 "
            pdb=" CB  PRO B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CA  PRO A 153 "
            pdb=" N   PRO A 153 "
            pdb=" C   PRO A 153 "
            pdb=" CB  PRO A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.03e-01
  chirality pdb=" CA  THR A 119 "
            pdb=" N   THR A 119 "
            pdb=" C   THR A 119 "
            pdb=" CB  THR A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.84e-01
  ... (remaining 1125 not shown)

  Planarity restraints: 1082
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 372 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO B 373 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 373 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 373 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 372 "    0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO A 373 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 373 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 373 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 106 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.23e+00
        pdb=" C   ALA B 106 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ALA B 106 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA B 107 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1079 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 3166
        2.97 -     3.45: 7094
        3.45 -     3.93: 10398
        3.93 -     4.42: 12130
        4.42 -     4.90: 19220
  Nonbonded interactions: 52008
  Sorted by model distance:
  nonbonded pdb=" O   ILE A   7 "
            pdb=" OG1 THR A  11 "
     model   vdw
     2.482 3.040
  nonbonded pdb=" O   ILE B   7 "
            pdb=" OG1 THR B  11 "
     model   vdw
     2.483 3.040
  nonbonded pdb=" OD1 ASN B 337 "
            pdb=" N   MET B 338 "
     model   vdw
     2.497 3.120
  nonbonded pdb=" OD1 ASN A 337 "
            pdb=" N   MET A 338 "
     model   vdw
     2.499 3.120
  nonbonded pdb=" ND2 ASN A 158 "
            pdb=" OD1 ASP A 370 "
     model   vdw
     2.520 3.120
  ... (remaining 52003 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 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:             7.890
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.940
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
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      :  0.007   0.060   6548  Z= 0.292
  Angle     :  0.680   6.172   8966  Z= 0.374
  Chirality :  0.043   0.156   1128
  Planarity :  0.005   0.039   1082
  Dihedral  : 10.049  53.140   2196
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.24), residues: 852
  helix: -0.97 (0.15), residues: 698
  sheet:  None (None), residues: 0
  loop :  0.96 (0.49), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  85 
 TYR   0.015   0.002   TYR A 294 
 PHE   0.016   0.002   PHE B 131 
 TRP   0.021   0.002   TRP B 399 
 HIS   0.006   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 ( 6548)
  covalent geometry    : angle       0.68013 ( 8966)
  hydrogen bonds       : bond        0.13439 (  529)
  hydrogen bonds       : angle       5.69399 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8689 (mmm) cc_final: 0.8206 (mmt)
REVERT: A  220 ASP cc_start: 0.6881 (t0) cc_final: 0.6515 (m-30)
REVERT: A  395 MET cc_start: 0.6551 (ttp) cc_final: 0.6328 (ttp)
REVERT: B  179 MET cc_start: 0.8686 (mmm) cc_final: 0.8240 (mmt)
REVERT: B  220 ASP cc_start: 0.6908 (t0) cc_final: 0.6625 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0764
  time to fit residues: 15.2331
Evaluate side-chains
  102 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.182864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.156503 restraints weight = 7751.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.160140 restraints weight = 4937.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.162655 restraints weight = 3649.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.164283 restraints weight = 2972.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.165533 restraints weight = 2575.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6548  Z= 0.149
  Angle     :  0.552   6.069   8966  Z= 0.285
  Chirality :  0.040   0.144   1128
  Planarity :  0.004   0.037   1082
  Dihedral  :  3.901  28.827    900
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  :  9.42 %
    Favored  : 87.69 %
  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:  1.21 (0.27), residues: 852
  helix:  0.93 (0.18), residues: 712
  sheet:  None (None), residues: 0
  loop :  0.68 (0.48), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.006   0.001   TYR A 401 
 PHE   0.011   0.001   PHE B 224 
 TRP   0.010   0.001   TRP B  78 
 HIS   0.005   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6548)
  covalent geometry    : angle       0.55200 ( 8966)
  hydrogen bonds       : bond        0.04628 (  529)
  hydrogen bonds       : angle       4.48025 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  205 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.6863 (t-90)
REVERT: A  220 ASP cc_start: 0.5918 (t0) cc_final: 0.5656 (m-30)
REVERT: A  395 MET cc_start: 0.6314 (ttp) cc_final: 0.6073 (ttp)
REVERT: B  205 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.6804 (t-90)
REVERT: B  220 ASP cc_start: 0.6032 (t0) cc_final: 0.5659 (m-30)
REVERT: B  395 MET cc_start: 0.6200 (ttp) cc_final: 0.5988 (ttp)
  outliers start: 19
  outliers final: 8
  residues processed: 129
  average time/residue: 0.0721
  time to fit residues: 12.8014
Evaluate side-chains
  111 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  397 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 46 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0060
   chunk 8 optimal weight:    0.3980
   chunk 74 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.3554

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.185748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.158880 restraints weight = 7704.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.162686 restraints weight = 4909.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.165125 restraints weight = 3621.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.167095 restraints weight = 2941.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.168296 restraints weight = 2524.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6548  Z= 0.117
  Angle     :  0.520   8.011   8966  Z= 0.262
  Chirality :  0.038   0.132   1128
  Planarity :  0.004   0.036   1082
  Dihedral  :  3.837  27.434    900
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.53 %
    Favored  : 84.35 %
  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:  2.09 (0.28), residues: 852
  helix:  1.58 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.69 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  85 
 TYR   0.006   0.001   TYR B 401 
 PHE   0.011   0.001   PHE A 224 
 TRP   0.008   0.001   TRP B  78 
 HIS   0.002   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6548)
  covalent geometry    : angle       0.51971 ( 8966)
  hydrogen bonds       : bond        0.04129 (  529)
  hydrogen bonds       : angle       4.29218 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  205 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.6901 (t-90)
REVERT: A  338 MET cc_start: 0.8149 (mmm) cc_final: 0.7938 (mmm)
REVERT: A  395 MET cc_start: 0.6113 (ttp) cc_final: 0.5893 (ttp)
REVERT: B  205 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.6841 (t-90)
REVERT: B  338 MET cc_start: 0.8152 (mmm) cc_final: 0.7939 (mmm)
REVERT: B  395 MET cc_start: 0.6187 (ttp) cc_final: 0.5976 (ttp)
  outliers start: 14
  outliers final: 7
  residues processed: 120
  average time/residue: 0.0631
  time to fit residues: 10.6269
Evaluate side-chains
  110 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  351 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.182179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.155342 restraints weight = 7809.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.159037 restraints weight = 5021.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.161456 restraints weight = 3730.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.163319 restraints weight = 3042.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.164178 restraints weight = 2621.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6548  Z= 0.145
  Angle     :  0.516   5.424   8966  Z= 0.264
  Chirality :  0.038   0.146   1128
  Planarity :  0.004   0.035   1082
  Dihedral  :  3.789  27.457    900
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 13.53 %
    Favored  : 83.28 %
  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:  2.42 (0.28), residues: 852
  helix:  1.82 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.72 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 424 
 TYR   0.007   0.001   TYR A 401 
 PHE   0.010   0.001   PHE B 224 
 TRP   0.008   0.001   TRP A  78 
 HIS   0.002   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6548)
  covalent geometry    : angle       0.51643 ( 8966)
  hydrogen bonds       : bond        0.04150 (  529)
  hydrogen bonds       : angle       4.26781 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  205 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.6925 (t-90)
REVERT: A  338 MET cc_start: 0.8209 (mmm) cc_final: 0.7921 (mmm)
REVERT: A  424 ARG cc_start: 0.8076 (tmt-80) cc_final: 0.7795 (tpt-90)
REVERT: B  205 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.6857 (t-90)
REVERT: B  220 ASP cc_start: 0.6011 (t0) cc_final: 0.5423 (m-30)
REVERT: B  338 MET cc_start: 0.8214 (mmm) cc_final: 0.7943 (mmm)
REVERT: B  424 ARG cc_start: 0.8086 (tmt-80) cc_final: 0.7831 (tpt-90)
  outliers start: 21
  outliers final: 14
  residues processed: 117
  average time/residue: 0.0678
  time to fit residues: 11.1472
Evaluate side-chains
  120 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  413 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 79 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 299 GLN
B 299 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.168083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.140771 restraints weight = 8136.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.144314 restraints weight = 5186.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.146791 restraints weight = 3858.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.148407 restraints weight = 3139.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.149542 restraints weight = 2727.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6548  Z= 0.120
  Angle     :  0.485   5.599   8966  Z= 0.249
  Chirality :  0.037   0.135   1128
  Planarity :  0.004   0.038   1082
  Dihedral  :  3.734  26.531    900
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.74 %
    Favored  : 82.37 %
  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:  2.71 (0.28), residues: 852
  helix:  2.02 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.78 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 424 
 TYR   0.004   0.001   TYR B 401 
 PHE   0.010   0.001   PHE B 224 
 TRP   0.007   0.001   TRP B  78 
 HIS   0.002   0.000   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6548)
  covalent geometry    : angle       0.48516 ( 8966)
  hydrogen bonds       : bond        0.03934 (  529)
  hydrogen bonds       : angle       4.20486 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  205 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.6946 (t-90)
REVERT: A  338 MET cc_start: 0.8299 (mmm) cc_final: 0.7888 (mmm)
REVERT: B  205 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.6871 (t-90)
REVERT: B  424 ARG cc_start: 0.8081 (tmt-80) cc_final: 0.7830 (tpt-90)
  outliers start: 19
  outliers final: 12
  residues processed: 119
  average time/residue: 0.0652
  time to fit residues: 10.9880
Evaluate side-chains
  117 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  385 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.176777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.149839 restraints weight = 8016.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.153118 restraints weight = 5125.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.155612 restraints weight = 3817.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.157136 restraints weight = 3117.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.158378 restraints weight = 2719.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6548  Z= 0.148
  Angle     :  0.517   6.171   8966  Z= 0.263
  Chirality :  0.038   0.144   1128
  Planarity :  0.004   0.038   1082
  Dihedral  :  3.724  26.781    900
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.20 %
    Favored  : 81.00 %
  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:  2.70 (0.28), residues: 852
  helix:  2.01 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.79 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 424 
 TYR   0.007   0.001   TYR B 290 
 PHE   0.011   0.001   PHE B 224 
 TRP   0.008   0.001   TRP B  78 
 HIS   0.001   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6548)
  covalent geometry    : angle       0.51699 ( 8966)
  hydrogen bonds       : bond        0.04067 (  529)
  hydrogen bonds       : angle       4.22705 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  205 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.6925 (t-90)
REVERT: A  338 MET cc_start: 0.8284 (mmm) cc_final: 0.7824 (mmm)
REVERT: A  424 ARG cc_start: 0.7666 (tpt-90) cc_final: 0.7072 (tpt-90)
REVERT: B  205 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.6857 (t-90)
  outliers start: 25
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0649
  time to fit residues: 11.0962
Evaluate side-chains
  121 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  413 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0570
   chunk 13 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.179310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.152353 restraints weight = 7936.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.155833 restraints weight = 5043.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.158093 restraints weight = 3726.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.159897 restraints weight = 3050.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.160975 restraints weight = 2647.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6548  Z= 0.118
  Angle     :  0.498   8.023   8966  Z= 0.252
  Chirality :  0.037   0.134   1128
  Planarity :  0.004   0.042   1082
  Dihedral  :  3.686  26.286    900
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.57 %
    Favored  : 80.55 %
  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: 852
  helix:  2.16 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.77 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 424 
 TYR   0.005   0.001   TYR B 290 
 PHE   0.011   0.001   PHE B 224 
 TRP   0.007   0.001   TRP B  78 
 HIS   0.001   0.000   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6548)
  covalent geometry    : angle       0.49800 ( 8966)
  hydrogen bonds       : bond        0.03791 (  529)
  hydrogen bonds       : angle       4.14983 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  205 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.6917 (t-90)
REVERT: A  338 MET cc_start: 0.8281 (mmm) cc_final: 0.7997 (mmm)
REVERT: B  205 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.6865 (t-90)
REVERT: B  289 MET cc_start: 0.7658 (tpt) cc_final: 0.7436 (tpt)
REVERT: B  385 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8771 (mp)
  outliers start: 19
  outliers final: 12
  residues processed: 116
  average time/residue: 0.0680
  time to fit residues: 11.0106
Evaluate side-chains
  113 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  385 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0870
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.178690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.151778 restraints weight = 7927.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.155105 restraints weight = 5057.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.157622 restraints weight = 3780.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.159127 restraints weight = 3081.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.160411 restraints weight = 2684.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6548  Z= 0.127
  Angle     :  0.509   8.555   8966  Z= 0.257
  Chirality :  0.037   0.138   1128
  Planarity :  0.004   0.038   1082
  Dihedral  :  3.667  26.373    900
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.26 %
    Favored  : 80.85 %
  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:  2.88 (0.28), residues: 852
  helix:  2.16 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.71 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 424 
 TYR   0.005   0.001   TYR B 290 
 PHE   0.011   0.001   PHE B 224 
 TRP   0.007   0.001   TRP B  78 
 HIS   0.001   0.000   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6548)
  covalent geometry    : angle       0.50913 ( 8966)
  hydrogen bonds       : bond        0.03857 (  529)
  hydrogen bonds       : angle       4.13961 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  338 MET cc_start: 0.8282 (mmm) cc_final: 0.8066 (mmm)
REVERT: A  385 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8771 (mp)
REVERT: B  148 ASP cc_start: 0.7915 (m-30) cc_final: 0.7673 (m-30)
REVERT: B  289 MET cc_start: 0.7594 (tpt) cc_final: 0.7356 (tpt)
REVERT: B  385 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8802 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0660
  time to fit residues: 10.7562
Evaluate side-chains
  116 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  385 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0000
   chunk 79 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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 = 0.3996 r_free = 0.3996 target = 0.178358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.151227 restraints weight = 8090.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.154708 restraints weight = 5152.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.157090 restraints weight = 3827.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.158693 restraints weight = 3129.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.159930 restraints weight = 2721.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6548  Z= 0.131
  Angle     :  0.514   9.242   8966  Z= 0.259
  Chirality :  0.037   0.139   1128
  Planarity :  0.004   0.039   1082
  Dihedral  :  3.670  26.299    900
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.72 %
    Favored  : 80.40 %
  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: 852
  helix:  2.17 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.71 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 424 
 TYR   0.005   0.001   TYR A 175 
 PHE   0.011   0.001   PHE B 224 
 TRP   0.007   0.001   TRP B  78 
 HIS   0.001   0.000   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6548)
  covalent geometry    : angle       0.51448 ( 8966)
  hydrogen bonds       : bond        0.03847 (  529)
  hydrogen bonds       : angle       4.13750 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  385 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8762 (mp)
REVERT: B  148 ASP cc_start: 0.8066 (m-30) cc_final: 0.7826 (m-30)
REVERT: B  205 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.6853 (t-90)
REVERT: B  385 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8778 (mp)
  outliers start: 19
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0616
  time to fit residues: 10.2265
Evaluate side-chains
  117 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  385 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.177688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.150797 restraints weight = 7874.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.154150 restraints weight = 5074.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.156460 restraints weight = 3802.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.157995 restraints weight = 3135.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.158874 restraints weight = 2740.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6548  Z= 0.142
  Angle     :  0.553  12.851   8966  Z= 0.273
  Chirality :  0.038   0.141   1128
  Planarity :  0.004   0.040   1082
  Dihedral  :  3.716  26.460    900
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.63 %
    Favored  : 79.48 %
  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: 852
  helix:  2.17 (0.19), residues: 716
  sheet:  None (None), residues: 0
  loop :  0.72 (0.49), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 424 
 TYR   0.010   0.001   TYR A 290 
 PHE   0.011   0.001   PHE B 224 
 TRP   0.007   0.001   TRP B  78 
 HIS   0.001   0.000   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6548)
  covalent geometry    : angle       0.55258 ( 8966)
  hydrogen bonds       : bond        0.03945 (  529)
  hydrogen bonds       : angle       4.15448 ( 1545)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  205 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.6885 (t-90)
REVERT: A  385 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8753 (mp)
REVERT: B  205 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.6868 (t-90)
REVERT: B  220 ASP cc_start: 0.6152 (t0) cc_final: 0.5000 (m-30)
REVERT: B  385 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8787 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0641
  time to fit residues: 10.7377
Evaluate side-chains
  119 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  205 HIS
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue  205 HIS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  385 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 43 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0870
   chunk 69 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7358

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.177753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.150807 restraints weight = 7911.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.154200 restraints weight = 5052.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.156610 restraints weight = 3757.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.158235 restraints weight = 3087.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.159274 restraints weight = 2684.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6548  Z= 0.137
  Angle     :  0.542  12.392   8966  Z= 0.268
  Chirality :  0.037   0.140   1128
  Planarity :  0.004   0.040   1082
  Dihedral  :  3.712  26.369    900
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.87 %
    Favored  : 79.94 %
  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:  2.94 (0.28), residues: 852
  helix:  2.19 (0.19), residues: 716
  sheet:  None (None), residues: 0
  loop :  0.72 (0.49), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 424 
 TYR   0.009   0.001   TYR A 290 
 PHE   0.011   0.001   PHE B 224 
 TRP   0.008   0.001   TRP A 386 
 HIS   0.001   0.000   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6548)
  covalent geometry    : angle       0.54183 ( 8966)
  hydrogen bonds       : bond        0.03896 (  529)
  hydrogen bonds       : angle       4.15503 ( 1545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1156.00 seconds
wall clock time: 20 minutes 36.32 seconds (1236.32 seconds total)