Starting phenix.real_space_refine
on Tue Mar  3 14:42:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t4k_25678/03_2026/7t4k_25678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t4k_25678/03_2026/7t4k_25678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t4k_25678/03_2026/7t4k_25678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t4k_25678/03_2026/7t4k_25678.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t4k_25678/03_2026/7t4k_25678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t4k_25678/03_2026/7t4k_25678.map"
  }
  resolution = 3.25
  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=   0.009
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
     P       2      5.49       5
     S      41      5.16       5
     C    3941      2.51       5
     N    1048      2.21       5
     O    1148      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6180
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 3039
          Classifications: {'peptide': 379}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 17, 'TRANS': 361}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 3141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 403, 3141
          Classifications: {'peptide': 403}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 22, 'TRANS': 380}
          Chain breaks: 4
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 114
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 67
  Time building chain proxies: 1.37, per 1000 atoms: 0.22
  Number of scatterers: 6180
  At special positions: 0
  Unit cell: (115.44, 78, 73.32, 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      41     16.00
     P       2     15.00
     O    1148      8.00
     N    1048      7.00
     C    3941      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: 0.50
  Conformation dependent library (CDL) restraints added in 323.2 milliseconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1514

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 6 sheets defined
      43.6% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 136
    Processing helix  chain 'A' and resid 155 through 157
      No H-bonds generated for 'chain 'A' and resid 155 through 157'
    Processing helix  chain 'A' and resid 203 through 215
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 307 through 328
      removed outlier: 3.567A  pdb=" N   HIS A 328 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 406 through 420
      removed outlier: 3.660A  pdb=" N   TRP A 410 " --> pdb=" O   LYS A 406 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA A 411 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   TYR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLU A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 443
      removed outlier: 3.545A  pdb=" N   LEU A 443 " --> pdb=" O   GLU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 462
      removed outlier: 3.566A  pdb=" N   LEU A 462 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 485
      removed outlier: 3.531A  pdb=" N   LEU A 483 " --> pdb=" O   ALA A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 491
      removed outlier: 3.925A  pdb=" N   LEU A 490 " --> pdb=" O   PRO A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 511
    Processing helix  chain 'A' and resid 542 through 555
      removed outlier: 3.703A  pdb=" N   ARG A 555 " --> pdb=" O   SER A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 574
    Processing helix  chain 'B' and resid 124 through 138
      removed outlier: 3.511A  pdb=" N   CYS B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLY B 138 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 157
      No H-bonds generated for 'chain 'B' and resid 155 through 157'
    Processing helix  chain 'B' and resid 203 through 211
    Processing helix  chain 'B' and resid 262 through 267
    Processing helix  chain 'B' and resid 268 through 271
    Processing helix  chain 'B' and resid 297 through 304
    Processing helix  chain 'B' and resid 307 through 328
      removed outlier: 3.728A  pdb=" N   HIS B 328 " --> pdb=" O   HIS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 393
    Processing helix  chain 'B' and resid 406 through 420
      removed outlier: 3.895A  pdb=" N   TYR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 462
    Processing helix  chain 'B' and resid 471 through 485
    Processing helix  chain 'B' and resid 486 through 491
      removed outlier: 3.747A  pdb=" N   LEU B 490 " --> pdb=" O   PRO B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 516
    Processing helix  chain 'B' and resid 542 through 555
      removed outlier: 3.835A  pdb=" N   ARG B 555 " --> pdb=" O   SER B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 574
    Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160
      removed outlier: 3.554A  pdb=" N   LYS A 177 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER A 251 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   LYS A 291 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   MET A 249 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 254 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296
    Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 372
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 167
      removed outlier: 3.558A  pdb=" N   LYS B 177 " --> pdb=" O   ASP B 160 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   SER B 175 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL B 173 " --> pdb=" O   PRO B 164 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 286 " --> pdb=" O   MET B 195 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 295 through 296
    Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 372

    264 hydrogen bonds defined for protein.
    765 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: 0.81

  Time building geometry restraints manager: 0.61 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: 1988
        1.34 -     1.46: 1125
        1.46 -     1.58: 3112
        1.58 -     1.69: 8
        1.69 -     1.81: 65
  Bond restraints: 6298
  Sorted by residual:
  bond pdb=" C   VAL B 216 "
       pdb=" N   PRO B 217 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.041 2.34e-02 1.83e+03 3.00e+00
  bond pdb=" C   LEU A 543 "
       pdb=" N   PRO A 544 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.024 1.51e-02 4.39e+03 2.60e+00
  bond pdb=" CB  ASP B 442 "
       pdb=" CG  ASP B 442 "
    ideal  model  delta    sigma   weight residual
    1.516  1.476  0.040 2.50e-02 1.60e+03 2.50e+00
  bond pdb=" CG  LEU A 571 "
       pdb=" CD1 LEU A 571 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.47e+00
  bond pdb=" C   LEU B 543 "
       pdb=" N   PRO B 544 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.020 1.28e-02 6.10e+03 2.35e+00
  ... (remaining 6293 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 8301
        2.34 -     4.68: 189
        4.68 -     7.02: 30
        7.02 -     9.36: 7
        9.36 -    11.70: 5
  Bond angle restraints: 8532
  Sorted by residual:
  angle pdb=" CA  GLU A 214 "
        pdb=" CB  GLU A 214 "
        pdb=" CG  GLU A 214 "
      ideal   model   delta    sigma   weight residual
     114.10  122.48   -8.38 2.00e+00 2.50e-01 1.75e+01
  angle pdb=" CA  MET B 249 "
        pdb=" CB  MET B 249 "
        pdb=" CG  MET B 249 "
      ideal   model   delta    sigma   weight residual
     114.10  122.10   -8.00 2.00e+00 2.50e-01 1.60e+01
  angle pdb=" N   GLU B 441 "
        pdb=" CA  GLU B 441 "
        pdb=" C   GLU B 441 "
      ideal   model   delta    sigma   weight residual
     111.36  115.39   -4.03 1.09e+00 8.42e-01 1.37e+01
  angle pdb=" CB  MET B 195 "
        pdb=" CG  MET B 195 "
        pdb=" SD  MET B 195 "
      ideal   model   delta    sigma   weight residual
     112.70  101.71   10.99 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" CB  GLN A 569 "
        pdb=" CG  GLN A 569 "
        pdb=" CD  GLN A 569 "
      ideal   model   delta    sigma   weight residual
     112.60  118.81   -6.21 1.70e+00 3.46e-01 1.33e+01
  ... (remaining 8527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 3498
       16.79 -    33.58: 296
       33.58 -    50.37: 46
       50.37 -    67.16: 7
       67.16 -    83.95: 6
  Dihedral angle restraints: 3853
    sinusoidal: 1537
      harmonic: 2316
  Sorted by residual:
  dihedral pdb=" CA  SER B 280 "
           pdb=" C   SER B 280 "
           pdb=" N   GLY B 281 "
           pdb=" CA  GLY B 281 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.06  -17.94     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ASN A 326 "
           pdb=" CB  ASN A 326 "
           pdb=" CG  ASN A 326 "
           pdb=" OD1 ASN A 326 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -173.25  -66.75     2      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CA  ASP B 121 "
           pdb=" CB  ASP B 121 "
           pdb=" CG  ASP B 121 "
           pdb=" OD1 ASP B 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.01   54.01     1      2.00e+01 2.50e-03 9.90e+00
  ... (remaining 3850 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 693
       0.048 -    0.095: 201
       0.095 -    0.143: 61
       0.143 -    0.191: 14
       0.191 -    0.239: 2
  Chirality restraints: 971
  Sorted by residual:
  chirality pdb=" CA  GLU A 158 "
            pdb=" N   GLU A 158 "
            pdb=" C   GLU A 158 "
            pdb=" CB  GLU A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ILE A 450 "
            pdb=" N   ILE A 450 "
            pdb=" C   ILE A 450 "
            pdb=" CB  ILE A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ILE B 257 "
            pdb=" N   ILE B 257 "
            pdb=" C   ILE B 257 "
            pdb=" CB  ILE B 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.70e-01
  ... (remaining 968 not shown)

  Planarity restraints: 1080
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 439 "    0.013 2.00e-02 2.50e+03   2.56e-02 6.58e+00
        pdb=" C   LYS B 439 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   LYS B 439 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLU B 440 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 125 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.53e+00
        pdb=" C   GLU B 125 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU B 125 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLY B 126 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 129 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.86e+00
        pdb=" C   TRP B 129 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   TRP B 129 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLU B 130 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1077 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1569
        2.81 -     3.33: 5732
        3.33 -     3.85: 9613
        3.85 -     4.38: 11703
        4.38 -     4.90: 20259
  Nonbonded interactions: 48876
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 346 "
            pdb=" OG1 THR B 352 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" ND2 ASN B 197 "
            pdb=" O   MET B 284 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" OE2 GLU A 320 "
            pdb=" NH2 ARG A 555 "
     model   vdw
     2.379 3.120
  nonbonded pdb=" OE2 GLU B 320 "
            pdb=" NH2 ARG B 555 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" O   TYR B 212 "
            pdb=" NH1 ARG B 239 "
     model   vdw
     2.397 3.120
  ... (remaining 48871 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 120 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 121 through 200 or (resid 201 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 202 through 223 or (resid 237 and (name N or name C \ 
A or name C or name O or name CB )) or resid 238 through 493 or (resid 494 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 495 through 574))
  selection = (chain 'B' and (resid 120 through 136 or resid 148 through 256 or (resid 282 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 283 through 511 o \ 
r resid 541 through 574))
}

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:             7.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.780
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
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      :  0.005   0.070   6298  Z= 0.209
  Angle     :  0.881  11.701   8532  Z= 0.468
  Chirality :  0.051   0.239    971
  Planarity :  0.006   0.046   1080
  Dihedral  : 12.764  83.950   2339
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.20 %
    Favored  : 98.65 %
  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:  0.51 (0.30), residues: 754
  helix:  1.27 (0.28), residues: 298
  sheet: -0.64 (0.49), residues: 114
  loop : -0.02 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 555 
 TYR   0.030   0.002   TYR A 373 
 PHE   0.032   0.002   PHE B 222 
 TRP   0.014   0.001   TRP A 567 
 HIS   0.005   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 6298)
  covalent geometry    : angle       0.88097 ( 8532)
  hydrogen bonds       : bond        0.15062 (  264)
  hydrogen bonds       : angle       5.76932 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  214 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7846 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0656
  time to fit residues: 9.1206
Evaluate side-chains
  82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0000
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
B 366 GLN
B 569 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.138127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.104575 restraints weight = 8783.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 3.01
r_work: 0.3086 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6298  Z= 0.146
  Angle     :  0.524   6.554   8532  Z= 0.271
  Chirality :  0.040   0.148    971
  Planarity :  0.004   0.038   1080
  Dihedral  :  5.862  78.809    847
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  5.55 %
    Favored  : 93.40 %
  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:  1.28 (0.30), residues: 754
  helix:  2.25 (0.28), residues: 301
  sheet: -0.42 (0.47), residues: 114
  loop :  0.11 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 555 
 TYR   0.015   0.001   TYR A 373 
 PHE   0.010   0.001   PHE A 253 
 TRP   0.006   0.001   TRP A 129 
 HIS   0.003   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6298)
  covalent geometry    : angle       0.52430 ( 8532)
  hydrogen bonds       : bond        0.04786 (  264)
  hydrogen bonds       : angle       4.45728 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7685 (mt0) cc_final: 0.7452 (mt0)
REVERT: A  167 LYS cc_start: 0.7999 (mptt) cc_final: 0.7698 (mttp)
REVERT: A  570 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7875 (mt-10)
REVERT: B  189 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7595 (mm110)
REVERT: B  284 MET cc_start: 0.8367 (mmm) cc_final: 0.7797 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 86
  average time/residue: 0.0676
  time to fit residues: 8.0416
Evaluate side-chains
  85 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  573 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 366 GLN
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.134968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.101477 restraints weight = 8764.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.97
r_work: 0.3044 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6298  Z= 0.186
  Angle     :  0.520   6.158   8532  Z= 0.266
  Chirality :  0.041   0.143    971
  Planarity :  0.004   0.037   1080
  Dihedral  :  5.852  76.686    847
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  7.65 %
    Favored  : 90.55 %
  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:  1.46 (0.31), residues: 754
  helix:  2.38 (0.29), residues: 303
  sheet: -0.36 (0.47), residues: 114
  loop :  0.23 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 555 
 TYR   0.019   0.001   TYR A 373 
 PHE   0.010   0.002   PHE A 287 
 TRP   0.005   0.001   TRP A 505 
 HIS   0.005   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 6298)
  covalent geometry    : angle       0.51959 ( 8532)
  hydrogen bonds       : bond        0.04540 (  264)
  hydrogen bonds       : angle       4.21967 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7726 (mt0) cc_final: 0.7504 (mt0)
REVERT: A  167 LYS cc_start: 0.7988 (mptt) cc_final: 0.7612 (mttp)
REVERT: A  214 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8088 (mm-30)
REVERT: A  360 CYS cc_start: 0.8562 (m) cc_final: 0.8352 (m)
REVERT: A  491 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7459 (mtmm)
REVERT: A  570 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7980 (mt-10)
REVERT: B  189 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7617 (mm110)
REVERT: B  203 ASN cc_start: 0.8383 (t0) cc_final: 0.8136 (t0)
REVERT: B  284 MET cc_start: 0.8414 (mmm) cc_final: 0.7808 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 86
  average time/residue: 0.0607
  time to fit residues: 7.3188
Evaluate side-chains
  83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 HIS
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 50 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 170 ASN
B 366 GLN
** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.134642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.101080 restraints weight = 8807.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.99
r_work: 0.3038 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6298  Z= 0.173
  Angle     :  0.499   5.491   8532  Z= 0.257
  Chirality :  0.040   0.141    971
  Planarity :  0.004   0.035   1080
  Dihedral  :  5.840  74.667    847
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  9.30 %
    Favored  : 89.06 %
  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:  1.47 (0.31), residues: 754
  helix:  2.41 (0.29), residues: 303
  sheet: -0.22 (0.49), residues: 104
  loop :  0.14 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 555 
 TYR   0.016   0.001   TYR A 373 
 PHE   0.010   0.001   PHE A 287 
 TRP   0.005   0.001   TRP A 505 
 HIS   0.004   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 6298)
  covalent geometry    : angle       0.49928 ( 8532)
  hydrogen bonds       : bond        0.04189 (  264)
  hydrogen bonds       : angle       4.10319 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7778 (mt0) cc_final: 0.7539 (mt0)
REVERT: A  167 LYS cc_start: 0.7958 (mptt) cc_final: 0.7562 (mttp)
REVERT: A  194 MET cc_start: 0.8251 (ppp) cc_final: 0.7951 (tmm)
REVERT: A  214 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7963 (mm-30)
REVERT: A  360 CYS cc_start: 0.8609 (m) cc_final: 0.8336 (m)
REVERT: A  494 TYR cc_start: 0.7203 (p90) cc_final: 0.6963 (p90)
REVERT: A  570 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7935 (mt-10)
REVERT: B  189 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7603 (mm110)
REVERT: B  203 ASN cc_start: 0.8371 (t0) cc_final: 0.8060 (t0)
REVERT: B  222 PHE cc_start: 0.8339 (m-10) cc_final: 0.8127 (m-10)
  outliers start: 11
  outliers final: 7
  residues processed: 83
  average time/residue: 0.0692
  time to fit residues: 7.8532
Evaluate side-chains
  82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  572 HIS
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 62 optimal weight:    0.3980
   chunk 20 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 76 optimal weight:    0.1980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 366 GLN
** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.134976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.101847 restraints weight = 8918.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.96
r_work: 0.3049 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6298  Z= 0.145
  Angle     :  0.495   7.175   8532  Z= 0.251
  Chirality :  0.039   0.141    971
  Planarity :  0.004   0.035   1080
  Dihedral  :  5.794  74.811    847
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.04 %
    Favored  : 88.01 %
  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:  1.54 (0.31), residues: 754
  helix:  2.48 (0.29), residues: 303
  sheet: -0.20 (0.49), residues: 100
  loop :  0.16 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 555 
 TYR   0.012   0.001   TYR A 373 
 PHE   0.011   0.001   PHE B 452 
 TRP   0.004   0.001   TRP A 505 
 HIS   0.003   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6298)
  covalent geometry    : angle       0.49456 ( 8532)
  hydrogen bonds       : bond        0.03887 (  264)
  hydrogen bonds       : angle       4.02624 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7772 (mt0) cc_final: 0.7536 (mt0)
REVERT: A  167 LYS cc_start: 0.7933 (mptt) cc_final: 0.7520 (mttp)
REVERT: A  194 MET cc_start: 0.8326 (ppp) cc_final: 0.7970 (tmm)
REVERT: A  214 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8033 (mm-30)
REVERT: A  360 CYS cc_start: 0.8610 (m) cc_final: 0.8293 (m)
REVERT: A  491 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7481 (mtmm)
REVERT: A  570 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7930 (mt-10)
REVERT: B  189 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7604 (mm110)
REVERT: B  203 ASN cc_start: 0.8377 (t0) cc_final: 0.8062 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 88
  average time/residue: 0.0764
  time to fit residues: 9.1180
Evaluate side-chains
  89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  491 LYS
Chi-restraints excluded: chain A residue  572 HIS
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  543 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 66 optimal weight:    0.1980
   chunk 69 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0370
   chunk 2 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
B 366 GLN
** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.135223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.102324 restraints weight = 8803.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.93
r_work: 0.3055 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6298  Z= 0.134
  Angle     :  0.486   5.664   8532  Z= 0.246
  Chirality :  0.039   0.142    971
  Planarity :  0.004   0.035   1080
  Dihedral  :  5.701  75.624    847
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 10.19 %
    Favored  : 87.41 %
  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:  1.62 (0.31), residues: 754
  helix:  2.51 (0.29), residues: 304
  sheet: -0.16 (0.49), residues: 100
  loop :  0.24 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 555 
 TYR   0.012   0.001   TYR A 373 
 PHE   0.010   0.001   PHE A 253 
 TRP   0.004   0.001   TRP A 505 
 HIS   0.003   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6298)
  covalent geometry    : angle       0.48557 ( 8532)
  hydrogen bonds       : bond        0.03670 (  264)
  hydrogen bonds       : angle       3.95877 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7761 (mt0) cc_final: 0.7511 (mt0)
REVERT: A  167 LYS cc_start: 0.7903 (mptt) cc_final: 0.7657 (mttp)
REVERT: A  194 MET cc_start: 0.8329 (ppp) cc_final: 0.8078 (tmm)
REVERT: A  214 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8181 (mm-30)
REVERT: A  360 CYS cc_start: 0.8589 (m) cc_final: 0.8292 (m)
REVERT: A  570 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7880 (mt-10)
REVERT: B  189 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7595 (mm110)
REVERT: B  203 ASN cc_start: 0.8389 (t0) cc_final: 0.8057 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 89
  average time/residue: 0.0752
  time to fit residues: 9.0027
Evaluate side-chains
  89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  572 HIS
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  543 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 41 optimal weight:    0.0030
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0670
   chunk 13 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.5528

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.134374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.102707 restraints weight = 8770.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.81
r_work: 0.3056 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6298  Z= 0.146
  Angle     :  0.501   6.718   8532  Z= 0.253
  Chirality :  0.039   0.142    971
  Planarity :  0.004   0.035   1080
  Dihedral  :  5.628  75.968    847
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.94 %
    Favored  : 87.11 %
  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:  1.61 (0.31), residues: 754
  helix:  2.51 (0.29), residues: 304
  sheet: -0.12 (0.49), residues: 100
  loop :  0.21 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 555 
 TYR   0.012   0.001   TYR A 373 
 PHE   0.011   0.001   PHE B 452 
 TRP   0.005   0.001   TRP B 567 
 HIS   0.003   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6298)
  covalent geometry    : angle       0.50086 ( 8532)
  hydrogen bonds       : bond        0.03726 (  264)
  hydrogen bonds       : angle       3.95477 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7744 (mt0) cc_final: 0.7498 (mt0)
REVERT: A  167 LYS cc_start: 0.7896 (mptt) cc_final: 0.7640 (mttp)
REVERT: A  194 MET cc_start: 0.8316 (ppp) cc_final: 0.7973 (tmm)
REVERT: A  214 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7941 (tp30)
REVERT: A  360 CYS cc_start: 0.8601 (m) cc_final: 0.8295 (m)
REVERT: A  570 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7884 (mt-10)
REVERT: B  189 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7607 (mm110)
REVERT: B  203 ASN cc_start: 0.8392 (t0) cc_final: 0.7999 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0819
  time to fit residues: 9.6634
Evaluate side-chains
  89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  543 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 65 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 68 optimal weight:    0.3980
   chunk 51 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 569 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 = 0.3671 r_free = 0.3671 target = 0.135082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.101645 restraints weight = 8867.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.99
r_work: 0.3045 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6298  Z= 0.147
  Angle     :  0.503   6.400   8532  Z= 0.253
  Chirality :  0.040   0.149    971
  Planarity :  0.004   0.035   1080
  Dihedral  :  5.547  76.254    847
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.24 %
    Favored  : 86.66 %
  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:  1.63 (0.31), residues: 754
  helix:  2.52 (0.29), residues: 304
  sheet: -0.09 (0.50), residues: 99
  loop :  0.21 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 555 
 TYR   0.012   0.001   TYR A 373 
 PHE   0.010   0.001   PHE B 452 
 TRP   0.004   0.001   TRP B 567 
 HIS   0.003   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6298)
  covalent geometry    : angle       0.50302 ( 8532)
  hydrogen bonds       : bond        0.03698 (  264)
  hydrogen bonds       : angle       3.94431 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7799 (mt0) cc_final: 0.7541 (mt0)
REVERT: A  167 LYS cc_start: 0.7956 (mptt) cc_final: 0.7691 (mttp)
REVERT: A  194 MET cc_start: 0.8351 (ppp) cc_final: 0.8015 (tmm)
REVERT: A  214 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7965 (tp30)
REVERT: A  360 CYS cc_start: 0.8615 (m) cc_final: 0.8008 (t)
REVERT: A  570 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7893 (mt-10)
REVERT: B  189 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7600 (mm110)
REVERT: B  203 ASN cc_start: 0.8416 (t0) cc_final: 0.8018 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 86
  average time/residue: 0.0704
  time to fit residues: 8.3092
Evaluate side-chains
  90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  572 HIS
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 72 optimal weight:    0.3980
   chunk 49 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0370
   chunk 67 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 43 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.135504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.102821 restraints weight = 8869.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.86
r_work: 0.3049 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6298  Z= 0.123
  Angle     :  0.491   6.702   8532  Z= 0.248
  Chirality :  0.039   0.142    971
  Planarity :  0.003   0.035   1080
  Dihedral  :  5.460  76.410    847
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.84 %
    Favored  : 86.66 %
  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:  1.68 (0.31), residues: 754
  helix:  2.58 (0.29), residues: 304
  sheet: -0.05 (0.50), residues: 99
  loop :  0.22 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 555 
 TYR   0.011   0.001   TYR B 482 
 PHE   0.010   0.001   PHE A 452 
 TRP   0.005   0.001   TRP B 567 
 HIS   0.002   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6298)
  covalent geometry    : angle       0.49089 ( 8532)
  hydrogen bonds       : bond        0.03466 (  264)
  hydrogen bonds       : angle       3.90803 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7769 (mt0) cc_final: 0.7528 (mt0)
REVERT: A  167 LYS cc_start: 0.7823 (mptt) cc_final: 0.7554 (mttp)
REVERT: A  194 MET cc_start: 0.8214 (ppp) cc_final: 0.7849 (tmm)
REVERT: A  214 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7873 (tp30)
REVERT: A  360 CYS cc_start: 0.8507 (m) cc_final: 0.7814 (t)
REVERT: A  570 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7799 (mt-10)
REVERT: B  189 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7576 (mm110)
REVERT: B  203 ASN cc_start: 0.8414 (t0) cc_final: 0.7994 (t0)
REVERT: B  213 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.6718 (mtt90)
  outliers start: 10
  outliers final: 9
  residues processed: 83
  average time/residue: 0.0753
  time to fit residues: 8.5504
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  572 HIS
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 64 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 569 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 = 0.3637 r_free = 0.3637 target = 0.133521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.101483 restraints weight = 8833.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.77
r_work: 0.3048 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6298  Z= 0.157
  Angle     :  0.521   8.545   8532  Z= 0.260
  Chirality :  0.040   0.143    971
  Planarity :  0.004   0.035   1080
  Dihedral  :  5.406  76.316    847
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.84 %
    Favored  : 86.66 %
  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:  1.58 (0.31), residues: 754
  helix:  2.51 (0.29), residues: 304
  sheet: -0.13 (0.50), residues: 100
  loop :  0.16 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 555 
 TYR   0.012   0.001   TYR B 482 
 PHE   0.009   0.001   PHE B 452 
 TRP   0.004   0.001   TRP A 505 
 HIS   0.003   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6298)
  covalent geometry    : angle       0.52113 ( 8532)
  hydrogen bonds       : bond        0.03744 (  264)
  hydrogen bonds       : angle       3.94979 (  765)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  152 GLN cc_start: 0.7830 (mt0) cc_final: 0.7580 (mt0)
REVERT: A  167 LYS cc_start: 0.7855 (mptt) cc_final: 0.7572 (mttp)
REVERT: A  194 MET cc_start: 0.8219 (ppp) cc_final: 0.7859 (tmm)
REVERT: A  214 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7843 (tp30)
REVERT: A  357 ASP cc_start: 0.8378 (t0) cc_final: 0.7789 (t0)
REVERT: A  360 CYS cc_start: 0.8496 (m) cc_final: 0.7857 (t)
REVERT: A  570 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7822 (mt-10)
REVERT: B  189 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7581 (mm110)
REVERT: B  203 ASN cc_start: 0.8447 (t0) cc_final: 0.8017 (t0)
REVERT: B  213 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.6851 (mtt90)
REVERT: B  423 ASP cc_start: 0.8259 (m-30) cc_final: 0.7843 (p0)
  outliers start: 10
  outliers final: 9
  residues processed: 82
  average time/residue: 0.0669
  time to fit residues: 7.6657
Evaluate side-chains
  85 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  449 THR
Chi-restraints excluded: chain B residue  515 CYS
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    0.1980
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 72 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B 569 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 = 0.3643 r_free = 0.3643 target = 0.133856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.101983 restraints weight = 8780.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.75
r_work: 0.3057 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6298  Z= 0.140
  Angle     :  0.512   8.502   8532  Z= 0.256
  Chirality :  0.039   0.142    971
  Planarity :  0.003   0.035   1080
  Dihedral  :  5.338  76.497    847
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.14 %
    Favored  : 86.21 %
  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 are not related in a simple way.
  whole:  1.62 (0.31), residues: 754
  helix:  2.54 (0.29), residues: 304
  sheet: -0.12 (0.50), residues: 100
  loop :  0.19 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 555 
 TYR   0.012   0.001   TYR B 482 
 PHE   0.010   0.001   PHE B 452 
 TRP   0.004   0.001   TRP B 567 
 HIS   0.003   0.001   HIS B 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6298)
  covalent geometry    : angle       0.51234 ( 8532)
  hydrogen bonds       : bond        0.03602 (  264)
  hydrogen bonds       : angle       3.91172 (  765)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1405.57 seconds
wall clock time: 24 minutes 46.53 seconds (1486.53 seconds total)