Starting phenix.real_space_refine
on Fri Aug 22 13:41:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q9i_18282/08_2025/8q9i_18282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q9i_18282/08_2025/8q9i_18282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q9i_18282/08_2025/8q9i_18282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q9i_18282/08_2025/8q9i_18282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q9i_18282/08_2025/8q9i_18282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q9i_18282/08_2025/8q9i_18282.cif"
  }
  resolution = 2.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       3      5.16       5
     C    1053      2.51       5
     N     303      2.21       5
     O     312      1.98       5
     H    1740      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3411
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "C"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "E"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1137
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Time building chain proxies: 0.94, per 1000 atoms: 0.28
  Number of scatterers: 3411
  At special positions: 0
  Unit cell: (69.065, 98.145, 39.258, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       3     16.00
     O     312      8.00
     N     303      7.00
     C    1053      6.00
     H    1740      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 50.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  384

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 50.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310
      removed outlier: 6.785A  pdb=" N   ILE A 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.851A  pdb=" N   VAL A 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.396A  pdb=" N   VAL A 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   LYS C 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   SER A 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330
      removed outlier: 5.991A  pdb=" N   GLY A 326 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   HIS C 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ILE A 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   GLY E 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ASN A 327 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342
      removed outlier: 6.857A  pdb=" N   GLU A 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   SER E 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LYS A 340 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.672A  pdb=" N   ASP A 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357
      removed outlier: 6.354A  pdb=" N   VAL A 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   LYS C 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   SER A 352 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
      removed outlier: 8.286A  pdb=" N   GLY C 355 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   ILE A 354 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LEU C 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   SER A 356 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.381A  pdb=" N   THR A 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ILE A 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377
      removed outlier: 6.741A  pdb=" N   LYS A 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   GLU E 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ILE A 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   HIS E 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   THR A 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   LEU E 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   LYS A 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)

    33 hydrogen bonds defined for protein.
    99 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.66

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 1737
        1.12 -     1.29: 279
        1.29 -     1.46: 486
        1.46 -     1.64: 933
        1.64 -     1.81: 3
  Bond restraints: 3438
  Sorted by residual:
  bond pdb=" CE1 PHE C 346 "
       pdb=" HE1 PHE C 346 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" NE2 GLN E 336 "
       pdb="HE21 GLN E 336 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" CE1 PHE A 346 "
       pdb=" HE1 PHE A 346 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" ND2 ASN A 327 "
       pdb="HD22 ASN A 327 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   VAL A 337 "
       pdb=" H   VAL A 337 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  ... (remaining 3433 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 5207
        2.40 -     4.79: 812
        4.79 -     7.19: 238
        7.19 -     9.59: 13
        9.59 -    11.99: 3
  Bond angle restraints: 6273
  Sorted by residual:
  angle pdb=" CB  HIS E 374 "
        pdb=" CG  HIS E 374 "
        pdb=" CD2 HIS E 374 "
      ideal   model   delta    sigma   weight residual
     131.20  125.10    6.10 1.30e+00 5.92e-01 2.20e+01
  angle pdb=" CB  HIS E 329 "
        pdb=" CG  HIS E 329 "
        pdb=" CD2 HIS E 329 "
      ideal   model   delta    sigma   weight residual
     131.20  125.13    6.07 1.30e+00 5.92e-01 2.18e+01
  angle pdb=" C   GLY C 334 "
        pdb=" N   GLY C 335 "
        pdb=" CA  GLY C 335 "
      ideal   model   delta    sigma   weight residual
     120.60  125.21   -4.61 1.01e+00 9.80e-01 2.08e+01
  angle pdb=" N   GLY A 326 "
        pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     110.69  116.62   -5.93 1.33e+00 5.65e-01 1.99e+01
  angle pdb=" CB  HIS C 329 "
        pdb=" CG  HIS C 329 "
        pdb=" CD2 HIS C 329 "
      ideal   model   delta    sigma   weight residual
     131.20  125.41    5.79 1.30e+00 5.92e-01 1.98e+01
  ... (remaining 6268 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.51: 1406
       15.51 -    31.01: 85
       31.01 -    46.51: 32
       46.51 -    62.01: 44
       62.01 -    77.51: 17
  Dihedral angle restraints: 1584
    sinusoidal: 903
      harmonic: 681
  Sorted by residual:
  dihedral pdb=" CA  SER C 316 "
           pdb=" C   SER C 316 "
           pdb=" N   LYS C 317 "
           pdb=" CA  LYS C 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.00   28.00     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  LYS E 347 "
           pdb=" C   LYS E 347 "
           pdb=" N   ASP E 348 "
           pdb=" CA  ASP E 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.00  -22.00     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  ILE C 360 "
           pdb=" C   ILE C 360 "
           pdb=" N   THR C 361 "
           pdb=" CA  THR C 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.18   20.82     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 1581 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.062: 154
       0.062 -    0.122: 68
       0.122 -    0.183: 24
       0.183 -    0.243: 8
       0.243 -    0.304: 4
  Chirality restraints: 258
  Sorted by residual:
  chirality pdb=" CA  LYS A 317 "
            pdb=" N   LYS A 317 "
            pdb=" C   LYS A 317 "
            pdb=" CB  LYS A 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CA  ASP E 348 "
            pdb=" N   ASP E 348 "
            pdb=" C   ASP E 348 "
            pdb=" CB  ASP E 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  LYS C 317 "
            pdb=" N   LYS C 317 "
            pdb=" C   LYS C 317 "
            pdb=" CB  LYS C 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 255 not shown)

  Planarity restraints: 495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 349 "    0.307 9.50e-02 1.11e+02   1.19e-01 9.29e+01
        pdb=" NE  ARG E 349 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 349 "    0.028 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 349 "    0.080 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 349 "   -0.013 2.00e-02 2.50e+03
        pdb="HH11 ARG E 349 "   -0.140 2.00e-02 2.50e+03
        pdb="HH12 ARG E 349 "    0.057 2.00e-02 2.50e+03
        pdb="HH21 ARG E 349 "   -0.040 2.00e-02 2.50e+03
        pdb="HH22 ARG E 349 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "   -0.108 2.00e-02 2.50e+03   4.95e-02 7.34e+01
        pdb=" CG  TYR C 310 "    0.007 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "    0.033 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "   -0.107 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 310 "    0.010 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 310 "    0.033 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 310 "    0.028 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 310 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "   -0.089 2.00e-02 2.50e+03   4.44e-02 5.91e+01
        pdb=" CG  TYR A 310 "    0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "    0.030 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "    0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "   -0.101 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 310 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 310 "    0.031 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 310 "    0.032 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 310 "    0.007 2.00e-02 2.50e+03
  ... (remaining 492 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 270
        2.18 -     2.79: 5939
        2.79 -     3.39: 8984
        3.39 -     4.00: 12050
        4.00 -     4.60: 16883
  Nonbonded interactions: 44126
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.577 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" OD2 ASP A 314 "
            pdb=" HZ1 LYS A 370 "
     model   vdw
     1.673 2.450
  nonbonded pdb=" OD2 ASP E 314 "
            pdb=" HZ3 LYS E 370 "
     model   vdw
     1.717 2.450
  ... (remaining 44121 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}

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:             4.430
  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:             0.020
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.290
  Find NCS groups from input model:        0.030
  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:6.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
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      :  0.011   0.035   1698  Z= 0.676
  Angle     :  1.796   6.814   2274  Z= 1.195
  Chirality :  0.085   0.304    258
  Planarity :  0.011   0.092    288
  Dihedral  : 11.444  77.511    648
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  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 aren not related in a simple way.
  whole: -1.34 (0.48), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.01 (0.37), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 349 
 TYR   0.098   0.033   TYR C 310 
 PHE   0.047   0.014   PHE E 346 
 HIS   0.014   0.004   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.01089 ( 1698)
  covalent geometry    : angle       1.79645 ( 2274)
  hydrogen bonds       : bond        0.07728 (   33)
  hydrogen bonds       : angle       6.94902 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6613 (mtmm)
REVERT: A  338 GLU cc_start: 0.7593 (tt0) cc_final: 0.7362 (mt-10)
REVERT: A  342 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7683 (mt-10)
REVERT: C  321 LYS cc_start: 0.7235 (ttpt) cc_final: 0.6692 (mttp)
REVERT: E  311 LYS cc_start: 0.6678 (ttpt) cc_final: 0.6345 (tmtt)
REVERT: E  320 SER cc_start: 0.8128 (t) cc_final: 0.7827 (p)
REVERT: E  321 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7258 (mttp)
REVERT: E  336 GLN cc_start: 0.8340 (tt0) cc_final: 0.8109 (tt0)
REVERT: E  342 GLU cc_start: 0.8292 (tt0) cc_final: 0.7751 (mt-10)
REVERT: E  345 ASP cc_start: 0.7908 (m-30) cc_final: 0.7614 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 1.4352
  time to fit residues: 108.8429
Evaluate side-chains
  47 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.135425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.124015 restraints weight = 6070.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 1.57
r_work: 0.3867 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3790 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.3325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1698  Z= 0.128
  Angle     :  0.590   4.177   2274  Z= 0.311
  Chirality :  0.049   0.152    258
  Planarity :  0.003   0.021    288
  Dihedral  :  6.310  16.436    222
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 0.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.10 %
    Favored  : 83.85 %
  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 aren not related in a simple way.
  whole: -1.42 (0.47), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.07 (0.36), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 349 
 TYR   0.006   0.001   TYR E 310 
 PHE   0.007   0.001   PHE A 346 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 1698)
  covalent geometry    : angle       0.58971 ( 2274)
  hydrogen bonds       : bond        0.02473 (   33)
  hydrogen bonds       : angle       4.58672 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7492 (mt-10)
REVERT: A  345 ASP cc_start: 0.7969 (t70) cc_final: 0.7657 (t70)
REVERT: C  342 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7767 (mt-10)
REVERT: E  342 GLU cc_start: 0.7866 (tt0) cc_final: 0.7514 (mt-10)
REVERT: E  349 ARG cc_start: 0.5573 (pmt-80) cc_final: 0.4714 (mtp85)
  outliers start: 2
  outliers final: 0
  residues processed: 47
  average time/residue: 1.6331
  time to fit residues: 77.6930
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.129578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.118893 restraints weight = 6314.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 1.52
r_work: 0.3806 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3727 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.4477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   1698  Z= 0.182
  Angle     :  0.591   4.175   2274  Z= 0.313
  Chirality :  0.051   0.153    258
  Planarity :  0.002   0.013    288
  Dihedral  :  5.656  14.054    222
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 0.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.23 %
    Favored  : 80.21 %
  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 aren not related in a simple way.
  whole: -1.51 (0.47), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.14 (0.36), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 349 
 TYR   0.010   0.003   TYR E 310 
 PHE   0.012   0.002   PHE A 346 
 HIS   0.003   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 1698)
  covalent geometry    : angle       0.59149 ( 2274)
  hydrogen bonds       : bond        0.02048 (   33)
  hydrogen bonds       : angle       4.31844 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7582 (mt-10)
REVERT: A  347 LYS cc_start: 0.8238 (mptp) cc_final: 0.8032 (mptp)
REVERT: C  311 LYS cc_start: 0.8400 (ttpt) cc_final: 0.7921 (ttmt)
REVERT: E  311 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7865 (pttt)
REVERT: E  342 GLU cc_start: 0.7893 (tt0) cc_final: 0.7554 (mt-10)
REVERT: E  349 ARG cc_start: 0.5718 (pmt-80) cc_final: 0.4808 (mtp85)
  outliers start: 3
  outliers final: 0
  residues processed: 42
  average time/residue: 1.2650
  time to fit residues: 53.9837
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  311 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0770
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.4076 r_free = 0.4076 target = 0.132362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.122045 restraints weight = 6061.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.46
r_work: 0.3857 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3782 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.4756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1698  Z= 0.087
  Angle     :  0.491   3.813   2274  Z= 0.252
  Chirality :  0.050   0.142    258
  Planarity :  0.002   0.012    288
  Dihedral  :  5.023  12.116    222
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 0.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.79 %
    Favored  : 80.21 %
  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 aren not related in a simple way.
  whole: -1.59 (0.46), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.20 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 349 
 TYR   0.005   0.001   TYR E 310 
 PHE   0.004   0.001   PHE C 346 
 HIS   0.002   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 1698)
  covalent geometry    : angle       0.49051 ( 2274)
  hydrogen bonds       : bond        0.01764 (   33)
  hydrogen bonds       : angle       3.79805 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7621 (mt-10)
REVERT: A  345 ASP cc_start: 0.7880 (t0) cc_final: 0.7602 (t70)
REVERT: C  311 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7871 (ttmt)
REVERT: C  345 ASP cc_start: 0.8011 (t70) cc_final: 0.7753 (t0)
REVERT: C  347 LYS cc_start: 0.8098 (mttp) cc_final: 0.7827 (mptt)
REVERT: C  376 LEU cc_start: 0.8638 (tt) cc_final: 0.8414 (tt)
REVERT: E  349 ARG cc_start: 0.5632 (pmt-80) cc_final: 0.4793 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 1.1914
  time to fit residues: 46.0277
Evaluate side-chains
  36 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.130409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.120103 restraints weight = 6252.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 1.45
r_work: 0.3839 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   1698  Z= 0.102
  Angle     :  0.492   3.971   2274  Z= 0.254
  Chirality :  0.050   0.144    258
  Planarity :  0.002   0.014    288
  Dihedral  :  4.807  12.148    222
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 0.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 18.75 %
    Favored  : 80.73 %
  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 aren not related in a simple way.
  whole: -1.55 (0.46), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.17 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG C 349 
 TYR   0.007   0.002   TYR E 310 
 PHE   0.005   0.001   PHE A 346 
 HIS   0.001   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 1698)
  covalent geometry    : angle       0.49173 ( 2274)
  hydrogen bonds       : bond        0.01648 (   33)
  hydrogen bonds       : angle       3.71670 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7584 (mt-10)
REVERT: A  345 ASP cc_start: 0.7914 (t0) cc_final: 0.7707 (t0)
REVERT: C  311 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7832 (ttmt)
REVERT: C  345 ASP cc_start: 0.7999 (t70) cc_final: 0.7766 (t0)
REVERT: C  347 LYS cc_start: 0.8064 (mttp) cc_final: 0.7810 (mptt)
REVERT: E  349 ARG cc_start: 0.5614 (pmt-80) cc_final: 0.4732 (mtt-85)
  outliers start: 1
  outliers final: 0
  residues processed: 37
  average time/residue: 1.2021
  time to fit residues: 45.2435
Evaluate side-chains
  36 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.130936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.120345 restraints weight = 6368.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 1.52
r_work: 0.3820 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.4917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   1698  Z= 0.135
  Angle     :  0.522   4.598   2274  Z= 0.271
  Chirality :  0.050   0.145    258
  Planarity :  0.002   0.019    288
  Dihedral  :  4.873  12.273    222
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 0.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 17.19 %
    Favored  : 82.29 %
  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 aren not related in a simple way.
  whole: -1.61 (0.45), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.22 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.008   0.002   TYR E 310 
 PHE   0.006   0.002   PHE C 346 
 HIS   0.002   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 1698)
  covalent geometry    : angle       0.52178 ( 2274)
  hydrogen bonds       : bond        0.01678 (   33)
  hydrogen bonds       : angle       3.87623 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7666 (mt-10)
REVERT: A  345 ASP cc_start: 0.7960 (t0) cc_final: 0.7747 (t70)
REVERT: C  311 LYS cc_start: 0.8312 (ttpt) cc_final: 0.7855 (tttt)
REVERT: C  345 ASP cc_start: 0.8083 (t70) cc_final: 0.7849 (t0)
REVERT: C  347 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7873 (mptt)
REVERT: E  349 ARG cc_start: 0.5652 (pmt-80) cc_final: 0.4662 (mtt180)
  outliers start: 1
  outliers final: 0
  residues processed: 38
  average time/residue: 1.1919
  time to fit residues: 46.0866
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  347 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 10 optimal weight:    0.0870
   chunk 8 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.1962

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.128702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.118251 restraints weight = 6651.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 1.54
r_work: 0.3822 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3741 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.5026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   1698  Z= 0.101
  Angle     :  0.489   4.122   2274  Z= 0.250
  Chirality :  0.050   0.142    258
  Planarity :  0.002   0.019    288
  Dihedral  :  4.665  11.844    222
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 0.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.71 %
    Favored  : 82.29 %
  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 aren not related in a simple way.
  whole: -1.63 (0.45), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG C 349 
 TYR   0.007   0.002   TYR E 310 
 PHE   0.004   0.001   PHE C 346 
 HIS   0.002   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 1698)
  covalent geometry    : angle       0.48946 ( 2274)
  hydrogen bonds       : bond        0.01552 (   33)
  hydrogen bonds       : angle       3.77720 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: C  311 LYS cc_start: 0.8308 (ttpt) cc_final: 0.7849 (tttt)
REVERT: C  345 ASP cc_start: 0.8029 (t70) cc_final: 0.7828 (t0)
REVERT: C  347 LYS cc_start: 0.8093 (mttp) cc_final: 0.7875 (mptt)
REVERT: E  349 ARG cc_start: 0.5645 (pmt-80) cc_final: 0.4684 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 1.1268
  time to fit residues: 44.7374
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.127837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.117458 restraints weight = 6488.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 1.53
r_work: 0.3807 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3731 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1698  Z= 0.111
  Angle     :  0.495   4.293   2274  Z= 0.255
  Chirality :  0.050   0.142    258
  Planarity :  0.002   0.018    288
  Dihedral  :  4.625  12.106    222
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 0.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.19 %
    Favored  : 82.81 %
  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 aren not related in a simple way.
  whole: -1.61 (0.45), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.22 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.007   0.002   TYR E 310 
 PHE   0.005   0.001   PHE A 346 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 1698)
  covalent geometry    : angle       0.49534 ( 2274)
  hydrogen bonds       : bond        0.01630 (   33)
  hydrogen bonds       : angle       3.77458 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: C  311 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7822 (tttt)
REVERT: C  345 ASP cc_start: 0.8011 (t70) cc_final: 0.7780 (t0)
REVERT: C  347 LYS cc_start: 0.8073 (mttp) cc_final: 0.7824 (mptt)
REVERT: E  349 ARG cc_start: 0.5624 (pmt-80) cc_final: 0.4672 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 1.1553
  time to fit residues: 45.8538
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.128929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.118717 restraints weight = 6566.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 1.54
r_work: 0.3825 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3746 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   1698  Z= 0.098
  Angle     :  0.488   4.173   2274  Z= 0.249
  Chirality :  0.050   0.141    258
  Planarity :  0.002   0.019    288
  Dihedral  :  4.528  11.524    222
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.71 %
    Favored  : 82.29 %
  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 aren not related in a simple way.
  whole: -1.60 (0.45), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.21 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG A 349 
 TYR   0.006   0.002   TYR E 310 
 PHE   0.004   0.001   PHE E 346 
 HIS   0.002   0.001   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 1698)
  covalent geometry    : angle       0.48838 ( 2274)
  hydrogen bonds       : bond        0.01563 (   33)
  hydrogen bonds       : angle       3.69299 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7769 (tmtt)
REVERT: A  342 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7599 (mt-10)
REVERT: C  311 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7812 (tttt)
REVERT: C  345 ASP cc_start: 0.8025 (t70) cc_final: 0.7811 (t0)
REVERT: C  347 LYS cc_start: 0.8102 (mttp) cc_final: 0.7889 (mptt)
REVERT: E  311 LYS cc_start: 0.8125 (tmtt) cc_final: 0.7782 (pttt)
REVERT: E  349 ARG cc_start: 0.5680 (pmt-80) cc_final: 0.4729 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 1.1816
  time to fit residues: 46.8838
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.129256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.119103 restraints weight = 6444.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 1.53
r_work: 0.3835 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.5169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   1698  Z= 0.091
  Angle     :  0.482   4.171   2274  Z= 0.245
  Chirality :  0.050   0.141    258
  Planarity :  0.002   0.020    288
  Dihedral  :  4.445  11.281    222
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.23 %
    Favored  : 81.77 %
  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 aren not related in a simple way.
  whole: -1.57 (0.45), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.18 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG C 349 
 TYR   0.006   0.001   TYR E 310 
 PHE   0.004   0.001   PHE E 346 
 HIS   0.002   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 1698)
  covalent geometry    : angle       0.48161 ( 2274)
  hydrogen bonds       : bond        0.01539 (   33)
  hydrogen bonds       : angle       3.60637 (   99)

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

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

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  426 Ramachandran restraints generated.
    213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7793 (tmtt)
REVERT: A  342 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7591 (mt-10)
REVERT: C  311 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7767 (ttmt)
REVERT: C  347 LYS cc_start: 0.8086 (mttp) cc_final: 0.7880 (mptt)
REVERT: E  311 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7791 (pttt)
REVERT: E  349 ARG cc_start: 0.5735 (pmt-80) cc_final: 0.4742 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 1.1850
  time to fit residues: 47.0004
Evaluate side-chains
  39 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.129349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.119089 restraints weight = 6290.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 1.46
r_work: 0.3820 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
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Overall statistics
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model-to-map fit, CC_mask: 0.8518
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   1698  Z= 0.106
  Angle     :  0.491   4.241   2274  Z= 0.252
  Chirality :  0.050   0.141    258
  Planarity :  0.002   0.022    288
  Dihedral  :  4.477  11.381    222
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.75 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.45), residues: 213
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.17 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG C 349 
 TYR   0.007   0.002   TYR E 310 
 PHE   0.005   0.001   PHE A 346 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 1698)
  covalent geometry    : angle       0.49057 ( 2274)
  hydrogen bonds       : bond        0.01595 (   33)
  hydrogen bonds       : angle       3.61238 (   99)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2295.99 seconds
wall clock time: 39 minutes 44.11 seconds (2384.11 seconds total)