Starting phenix.real_space_refine
on Tue Mar 11 17:46:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uyf_42804/03_2025/8uyf_42804.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uyf_42804/03_2025/8uyf_42804.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uyf_42804/03_2025/8uyf_42804.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uyf_42804/03_2025/8uyf_42804.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uyf_42804/03_2025/8uyf_42804.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uyf_42804/03_2025/8uyf_42804.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.007 sd=   0.044
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      44      5.16       5
     C    4124      2.51       5
     N    1090      2.21       5
     O    1200      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6460
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3231
          Classifications: {'peptide': 400}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 381}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 3229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3229
          Classifications: {'peptide': 401}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 18, 'TRANS': 382}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 4.53, per 1000 atoms: 0.70
  Number of scatterers: 6460
  At special positions: 0
  Unit cell: (115.544, 75.952, 76.76, 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      44     16.00
     P       2     15.00
     O    1200      8.00
     N    1090      7.00
     C    4124      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: 1.59
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1554

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 7 sheets defined
      43.2% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 137
    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: 3.533A  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: 3.750A  pdb=" N   TYR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLU A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 462
    Processing helix  chain 'A' and resid 471 through 485
    Processing helix  chain 'A' and resid 486 through 490
    Processing helix  chain 'A' and resid 498 through 515
    Processing helix  chain 'A' and resid 542 through 556
      removed outlier: 3.701A  pdb=" N   ARG A 555 " --> pdb=" O   SER A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 574
      removed outlier: 3.779A  pdb=" N   HIS A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 137
      removed outlier: 4.242A  pdb=" N   GLY B 126 " --> pdb=" O   ASP B 122 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ILE B 127 " --> pdb=" O   GLU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 215
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 4.416A  pdb=" N   ASP B 235 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 304
    Processing helix  chain 'B' and resid 307 through 328
      removed outlier: 3.556A  pdb=" N   HIS B 328 " --> pdb=" O   HIS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 361
      removed outlier: 4.542A  pdb=" N   CYS B 360 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 393
    Processing helix  chain 'B' and resid 406 through 420
      removed outlier: 3.979A  pdb=" N   TYR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 443
    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: 3.738A  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: 3.773A  pdb=" N   ARG B 555 " --> pdb=" O   SER B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 574
      removed outlier: 3.630A  pdb=" N   HIS B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160
      removed outlier: 3.597A  pdb=" N   SER A 251 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   LYS A 291 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   MET A 249 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 254 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296
      removed outlier: 3.604A  pdb=" N   CYS A 295 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 372
    Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 166
      removed outlier: 3.651A  pdb=" N   SER B 251 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   LYS B 291 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   MET B 249 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 295 through 296
      removed outlier: 3.573A  pdb=" N   CYS B 295 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 372

    290 hydrogen bonds defined for protein.
    831 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.03

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2089
        1.34 -     1.46: 1405
        1.46 -     1.58: 3019
        1.58 -     1.69: 6
        1.69 -     1.81: 68
  Bond restraints: 6587
  Sorted by residual:
  bond pdb=" OG1 TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" OG1 TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.92e+01
  bond pdb=" O1P TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.525  1.610 -0.085 2.00e-02 2.50e+03 1.79e+01
  bond pdb=" O2P TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" O3P TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.67e+01
  ... (remaining 6582 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 8862
        2.58 -     5.16: 46
        5.16 -     7.74: 3
        7.74 -    10.32: 2
       10.32 -    12.90: 2
  Bond angle restraints: 8915
  Sorted by residual:
  angle pdb=" CB  TPO B 305 "
        pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
      ideal   model   delta    sigma   weight residual
     119.31  106.41   12.90 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" CB  TPO A 305 "
        pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
      ideal   model   delta    sigma   weight residual
     119.31  107.04   12.27 3.00e+00 1.11e-01 1.67e+01
  angle pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
        pdb=" O1P TPO A 305 "
      ideal   model   delta    sigma   weight residual
     100.43  109.64   -9.21 3.00e+00 1.11e-01 9.42e+00
  angle pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
        pdb=" O1P TPO B 305 "
      ideal   model   delta    sigma   weight residual
     100.43  109.40   -8.97 3.00e+00 1.11e-01 8.95e+00
  angle pdb=" C   THR A 215 "
        pdb=" N   VAL A 216 "
        pdb=" CA  VAL A 216 "
      ideal   model   delta    sigma   weight residual
     120.33  122.15   -1.82 8.00e-01 1.56e+00 5.16e+00
  ... (remaining 8910 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.76: 3722
       11.76 -    23.53: 232
       23.53 -    35.29: 53
       35.29 -    47.06: 16
       47.06 -    58.82: 10
  Dihedral angle restraints: 4033
    sinusoidal: 1653
      harmonic: 2380
  Sorted by residual:
  dihedral pdb=" CB  ARG B 554 "
           pdb=" CG  ARG B 554 "
           pdb=" CD  ARG B 554 "
           pdb=" NE  ARG B 554 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.26   56.26     3      1.50e+01 4.44e-03 9.39e+00
  dihedral pdb=" N   GLU B 376 "
           pdb=" CA  GLU B 376 "
           pdb=" CB  GLU B 376 "
           pdb=" CG  GLU B 376 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.69  -55.31     3      1.50e+01 4.44e-03 9.34e+00
  dihedral pdb=" N   LEU B 560 "
           pdb=" CA  LEU B 560 "
           pdb=" CB  LEU B 560 "
           pdb=" CG  LEU B 560 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.70   54.70     3      1.50e+01 4.44e-03 9.30e+00
  ... (remaining 4030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 640
       0.028 -    0.055: 235
       0.055 -    0.083: 77
       0.083 -    0.110: 37
       0.110 -    0.138: 12
  Chirality restraints: 1001
  Sorted by residual:
  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    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE B 450 "
            pdb=" N   ILE B 450 "
            pdb=" C   ILE B 450 "
            pdb=" CB  ILE B 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  chirality pdb=" CA  VAL B 172 "
            pdb=" N   VAL B 172 "
            pdb=" C   VAL B 172 "
            pdb=" CB  VAL B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 998 not shown)

  Planarity restraints: 1131
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 450 "    0.023 5.00e-02 4.00e+02   3.47e-02 1.93e+00
        pdb=" N   PRO B 451 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 450 "   -0.020 5.00e-02 4.00e+02   3.08e-02 1.52e+00
        pdb=" N   PRO A 451 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 485 "    0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO A 486 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 486 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 486 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1128 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 1894
        2.82 -     3.34: 5921
        3.34 -     3.86: 10404
        3.86 -     4.38: 12995
        4.38 -     4.90: 21551
  Nonbonded interactions: 52765
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 491 "
            pdb=" O   ASN A 493 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" N   ASP A 379 "
            pdb=" OD1 ASP A 379 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O   PHE B 452 "
            pdb=" ND2 ASN B 456 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" N   ASP A 423 "
            pdb=" OD1 ASP A 423 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" O   PRO A 389 "
            pdb=" ND2 ASN A 393 "
     model   vdw
     2.346 3.120
  ... (remaining 52760 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 573 or (resid 574 and (name N or name CA or name C or n \ 
ame O or name CB ))))
  selection = (chain 'B' and (resid 120 through 515 or resid 540 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:             0.730
  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:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.250
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  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:13.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   6587  Z= 0.181
  Angle     :  0.515  12.902   8915  Z= 0.264
  Chirality :  0.037   0.138   1001
  Planarity :  0.003   0.035   1131
  Dihedral  :  9.080  58.823   2479
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  4.18 %
    Favored  : 94.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.30), residues: 775
  helix:  2.01 (0.29), residues: 317
  sheet: -0.42 (0.48), residues: 123
  loop :  0.10 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 484 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.007   0.001   PHE A 253 
 TYR   0.008   0.001   TYR A 174 
 ARG   0.002   0.000   ARG B 374 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 174
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 ASP cc_start: 0.7121 (m-30) cc_final: 0.6886 (m-30)
REVERT: A  178 LEU cc_start: 0.8312 (mt) cc_final: 0.7799 (pp)
REVERT: A  201 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8031 (mm-30)
REVERT: A  215 THR cc_start: 0.9419 (p) cc_final: 0.9182 (p)
REVERT: A  232 ASN cc_start: 0.8509 (m-40) cc_final: 0.8184 (m110)
REVERT: A  282 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7395 (mpp-170)
REVERT: A  384 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.7923 (mtm110)
REVERT: A  395 LYS cc_start: 0.8681 (mttt) cc_final: 0.8441 (mtpm)
REVERT: A  500 ASN cc_start: 0.7923 (t0) cc_final: 0.7403 (t0)
REVERT: A  563 LYS cc_start: 0.8363 (mttt) cc_final: 0.8035 (mptt)
REVERT: A  570 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6865 (mp0)
REVERT: B  133 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7638 (pp20)
REVERT: B  178 LEU cc_start: 0.7388 (mt) cc_final: 0.7133 (pt)
REVERT: B  179 LYS cc_start: 0.7529 (tttt) cc_final: 0.7248 (tppt)
REVERT: B  209 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8293 (mttp)
REVERT: B  264 LYS cc_start: 0.6976 (mttt) cc_final: 0.6739 (mmmt)
REVERT: B  338 ASP cc_start: 0.8435 (t0) cc_final: 0.8168 (t0)
REVERT: B  366 GLN cc_start: 0.8720 (mt0) cc_final: 0.8508 (pt0)
REVERT: B  379 ASP cc_start: 0.8282 (p0) cc_final: 0.8052 (OUTLIER)
REVERT: B  558 LEU cc_start: 0.8735 (tp) cc_final: 0.8521 (tm)
REVERT: B  559 HIS cc_start: 0.6704 (t70) cc_final: 0.6496 (t70)
REVERT: B  563 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8408 (mtpp)
  outliers start: 8
  outliers final: 2
  residues processed: 179
  average time/residue: 1.2708
  time to fit residues: 238.2054
Evaluate side-chains
  134 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  496 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 197 ASN
B 339 ASN
B 378 GLN
B 467 ASN
B 504 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.118987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.105520 restraints weight = 9769.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.29
r_work: 0.3287 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6587  Z= 0.181
  Angle     :  0.521   4.829   8915  Z= 0.275
  Chirality :  0.040   0.141   1001
  Planarity :  0.004   0.034   1131
  Dihedral  :  3.990  38.448    870
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 11.44 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.30), residues: 775
  helix:  2.23 (0.28), residues: 328
  sheet: -0.31 (0.46), residues: 124
  loop :  0.22 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.003   0.001   HIS B 559 
 PHE   0.012   0.001   PHE A 452 
 TYR   0.016   0.001   TYR A 494 
 ARG   0.005   0.001   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.8071 (mt) cc_final: 0.7570 (pp)
REVERT: A  237 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8294 (ptpp)
REVERT: A  282 ARG cc_start: 0.8123 (mtp180) cc_final: 0.7440 (mtt90)
REVERT: A  384 ARG cc_start: 0.8818 (mtp-110) cc_final: 0.8280 (mtm110)
REVERT: A  395 LYS cc_start: 0.8866 (mttt) cc_final: 0.8601 (mtpp)
REVERT: A  563 LYS cc_start: 0.8451 (mttt) cc_final: 0.8077 (mmtm)
REVERT: B  133 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7719 (pp20)
REVERT: B  174 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8168 (m-80)
REVERT: B  178 LEU cc_start: 0.7371 (mt) cc_final: 0.7144 (pt)
REVERT: B  179 LYS cc_start: 0.7769 (tttt) cc_final: 0.7490 (tppt)
REVERT: B  209 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8475 (mtmm)
REVERT: B  264 LYS cc_start: 0.7199 (mttt) cc_final: 0.6930 (mmmt)
REVERT: B  284 MET cc_start: 0.8490 (tpp) cc_final: 0.7862 (tpp)
REVERT: B  338 ASP cc_start: 0.8687 (t0) cc_final: 0.8373 (t0)
REVERT: B  366 GLN cc_start: 0.8771 (mt0) cc_final: 0.8232 (pt0)
REVERT: B  563 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8619 (mtpp)
  outliers start: 19
  outliers final: 10
  residues processed: 150
  average time/residue: 1.1755
  time to fit residues: 185.0342
Evaluate side-chains
  129 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  510 SER
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  379 ASP
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 74 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 197 ASN
B 339 ASN
B 378 GLN
B 504 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.119717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.106038 restraints weight = 9693.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.33
r_work: 0.3284 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6587  Z= 0.164
  Angle     :  0.482   5.468   8915  Z= 0.251
  Chirality :  0.039   0.141   1001
  Planarity :  0.003   0.033   1131
  Dihedral  :  3.970  37.980    870
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.67 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.30), residues: 775
  helix:  2.35 (0.28), residues: 323
  sheet: -0.15 (0.47), residues: 117
  loop :  0.13 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 572 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.933 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7970 (mt) cc_final: 0.7477 (pp)
REVERT: A  237 LYS cc_start: 0.8589 (ptpt) cc_final: 0.8319 (ptpp)
REVERT: A  282 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7555 (mpt90)
REVERT: A  384 ARG cc_start: 0.8857 (mtp-110) cc_final: 0.8278 (mtm110)
REVERT: A  395 LYS cc_start: 0.8814 (mttt) cc_final: 0.8576 (mtpm)
REVERT: A  431 MET cc_start: 0.5011 (OUTLIER) cc_final: 0.4785 (ttt)
REVERT: A  440 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7087 (mp0)
REVERT: A  563 LYS cc_start: 0.8517 (mttt) cc_final: 0.8105 (mmtm)
REVERT: B  178 LEU cc_start: 0.7341 (mt) cc_final: 0.7136 (pt)
REVERT: B  179 LYS cc_start: 0.7653 (tttt) cc_final: 0.7320 (tppt)
REVERT: B  209 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8384 (mtmm)
REVERT: B  264 LYS cc_start: 0.7172 (mttt) cc_final: 0.6936 (mmmt)
REVERT: B  284 MET cc_start: 0.8517 (tpp) cc_final: 0.7882 (tpp)
REVERT: B  338 ASP cc_start: 0.8709 (t0) cc_final: 0.8354 (t0)
REVERT: B  366 GLN cc_start: 0.8806 (mt0) cc_final: 0.8489 (pt0)
REVERT: B  563 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8657 (mtpp)
  outliers start: 14
  outliers final: 6
  residues processed: 135
  average time/residue: 1.2968
  time to fit residues: 183.0611
Evaluate side-chains
  124 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 197 ASN
B 339 ASN
B 378 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.120257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.106671 restraints weight = 9786.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.31
r_work: 0.3299 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6587  Z= 0.153
  Angle     :  0.488  10.318   8915  Z= 0.249
  Chirality :  0.038   0.140   1001
  Planarity :  0.003   0.033   1131
  Dihedral  :  3.656  14.834    868
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.67 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.30), residues: 775
  helix:  2.46 (0.28), residues: 323
  sheet: -0.11 (0.47), residues: 117
  loop :  0.09 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7893 (mt) cc_final: 0.7405 (pp)
REVERT: A  282 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7555 (mpt90)
REVERT: A  395 LYS cc_start: 0.8821 (mttt) cc_final: 0.8573 (mtpm)
REVERT: A  440 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6992 (mp0)
REVERT: A  504 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7902 (mp10)
REVERT: A  543 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8192 (tm)
REVERT: A  563 LYS cc_start: 0.8511 (mttt) cc_final: 0.8102 (mmtm)
REVERT: B  174 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8312 (m-80)
REVERT: B  179 LYS cc_start: 0.7527 (tttt) cc_final: 0.7286 (tppt)
REVERT: B  264 LYS cc_start: 0.7155 (mttt) cc_final: 0.6922 (mmmt)
REVERT: B  338 ASP cc_start: 0.8666 (t0) cc_final: 0.8306 (t0)
REVERT: B  366 GLN cc_start: 0.8870 (mt0) cc_final: 0.8309 (pt0)
REVERT: B  563 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8586 (mtpp)
  outliers start: 18
  outliers final: 5
  residues processed: 130
  average time/residue: 1.2948
  time to fit residues: 176.2301
Evaluate side-chains
  123 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0050
   chunk 8 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 197 ASN
B 339 ASN
B 378 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.120625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.107281 restraints weight = 9822.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.27
r_work: 0.3308 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6587  Z= 0.148
  Angle     :  0.471   8.170   8915  Z= 0.240
  Chirality :  0.038   0.139   1001
  Planarity :  0.003   0.033   1131
  Dihedral  :  3.575  14.900    868
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.92 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.30), residues: 775
  helix:  2.58 (0.28), residues: 323
  sheet: -0.05 (0.47), residues: 117
  loop :  0.08 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.011   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.007   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7867 (mt) cc_final: 0.7359 (pp)
REVERT: A  282 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7533 (mpt90)
REVERT: A  395 LYS cc_start: 0.8823 (mttt) cc_final: 0.8583 (mtpm)
REVERT: A  440 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7019 (mp0)
REVERT: A  504 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7836 (mp10)
REVERT: A  543 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8168 (tm)
REVERT: A  563 LYS cc_start: 0.8515 (mttt) cc_final: 0.8111 (mmtm)
REVERT: B  174 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8261 (m-80)
REVERT: B  179 LYS cc_start: 0.7457 (tttt) cc_final: 0.7177 (tppt)
REVERT: B  213 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7808 (mtp180)
REVERT: B  284 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7830 (tpp)
REVERT: B  338 ASP cc_start: 0.8641 (t0) cc_final: 0.8290 (t0)
REVERT: B  366 GLN cc_start: 0.8851 (mt0) cc_final: 0.8466 (pt0)
REVERT: B  377 ASP cc_start: 0.7945 (t0) cc_final: 0.7021 (t0)
REVERT: B  563 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8571 (mtpp)
  outliers start: 19
  outliers final: 8
  residues processed: 137
  average time/residue: 1.2340
  time to fit residues: 177.2413
Evaluate side-chains
  130 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  213 ARG
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 197 ASN
B 378 GLN
B 569 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.120446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.106967 restraints weight = 9761.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.27
r_work: 0.3302 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6587  Z= 0.166
  Angle     :  0.514  15.430   8915  Z= 0.254
  Chirality :  0.039   0.139   1001
  Planarity :  0.003   0.034   1131
  Dihedral  :  3.580  15.577    868
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.62 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.30), residues: 775
  helix:  2.60 (0.28), residues: 323
  sheet:  0.01 (0.47), residues: 117
  loop :  0.05 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 505 
 HIS   0.004   0.001   HIS A 572 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.007   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.7802 (mt) cc_final: 0.7293 (pp)
REVERT: A  237 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8316 (ptpp)
REVERT: A  282 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7454 (mtt90)
REVERT: A  384 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8373 (mtm110)
REVERT: A  395 LYS cc_start: 0.8824 (mttt) cc_final: 0.8586 (mtpm)
REVERT: A  440 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7022 (mp0)
REVERT: A  543 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8188 (tm)
REVERT: A  563 LYS cc_start: 0.8519 (mttt) cc_final: 0.8117 (mmtm)
REVERT: B  133 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7696 (mt-10)
REVERT: B  174 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8263 (m-80)
REVERT: B  179 LYS cc_start: 0.7455 (tttt) cc_final: 0.7170 (tppt)
REVERT: B  284 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7808 (tpp)
REVERT: B  338 ASP cc_start: 0.8650 (t0) cc_final: 0.8288 (t0)
REVERT: B  366 GLN cc_start: 0.8894 (mt0) cc_final: 0.8330 (pt0)
REVERT: B  563 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8625 (mtpp)
  outliers start: 16
  outliers final: 11
  residues processed: 128
  average time/residue: 1.1585
  time to fit residues: 155.8413
Evaluate side-chains
  128 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  569 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 6 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 70 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 ASN
B 378 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 = 0.3604 r_free = 0.3604 target = 0.121081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.107580 restraints weight = 9775.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.29
r_work: 0.3313 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6587  Z= 0.140
  Angle     :  0.512  16.656   8915  Z= 0.253
  Chirality :  0.039   0.140   1001
  Planarity :  0.003   0.034   1131
  Dihedral  :  3.534  15.339    868
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.46 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.30), residues: 775
  helix:  2.62 (0.28), residues: 323
  sheet:  0.01 (0.47), residues: 117
  loop :  0.07 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 505 
 HIS   0.005   0.001   HIS A 572 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.022   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7709 (mt) cc_final: 0.7206 (pp)
REVERT: A  237 LYS cc_start: 0.8575 (ptpt) cc_final: 0.8292 (ptpp)
REVERT: A  261 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6795 (mm-40)
REVERT: A  282 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7450 (mtt90)
REVERT: A  395 LYS cc_start: 0.8825 (mttt) cc_final: 0.8586 (mtpm)
REVERT: A  440 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7017 (mp0)
REVERT: A  504 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7902 (mp10)
REVERT: A  543 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8190 (tm)
REVERT: A  563 LYS cc_start: 0.8501 (mttt) cc_final: 0.8095 (mmtm)
REVERT: B  174 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8332 (m-80)
REVERT: B  179 LYS cc_start: 0.7397 (tttt) cc_final: 0.7106 (tppt)
REVERT: B  284 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7799 (tpp)
REVERT: B  338 ASP cc_start: 0.8628 (t0) cc_final: 0.8289 (t0)
REVERT: B  366 GLN cc_start: 0.8868 (mt0) cc_final: 0.8488 (pt0)
REVERT: B  377 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7347 (t70)
REVERT: B  563 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8612 (mtpp)
  outliers start: 17
  outliers final: 6
  residues processed: 127
  average time/residue: 1.2344
  time to fit residues: 164.4965
Evaluate side-chains
  128 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0870
   chunk 1 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0980
   chunk 44 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
A 572 HIS
B 197 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.121151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.107891 restraints weight = 9811.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.25
r_work: 0.3316 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6587  Z= 0.146
  Angle     :  0.529  16.851   8915  Z= 0.260
  Chirality :  0.038   0.139   1001
  Planarity :  0.003   0.034   1131
  Dihedral  :  3.480  15.338    868
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.46 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.30), residues: 775
  helix:  2.66 (0.28), residues: 323
  sheet:  0.00 (0.47), residues: 117
  loop :  0.08 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 572 
 PHE   0.010   0.001   PHE B 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.007   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A  163 GLU cc_start: 0.8015 (pm20) cc_final: 0.7743 (pm20)
REVERT: A  178 LEU cc_start: 0.7614 (mt) cc_final: 0.7143 (pp)
REVERT: A  235 ASP cc_start: 0.8109 (m-30) cc_final: 0.7836 (m-30)
REVERT: A  237 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8290 (ptpp)
REVERT: A  282 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7439 (mtt90)
REVERT: A  395 LYS cc_start: 0.8822 (mttt) cc_final: 0.8563 (mtpm)
REVERT: A  440 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7011 (mp0)
REVERT: A  504 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7870 (mp10)
REVERT: A  543 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8186 (tm)
REVERT: A  563 LYS cc_start: 0.8503 (mttt) cc_final: 0.8089 (mmtm)
REVERT: B  133 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7722 (mt-10)
REVERT: B  174 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8311 (m-80)
REVERT: B  179 LYS cc_start: 0.7313 (tttt) cc_final: 0.7024 (tppt)
REVERT: B  213 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7627 (mtp180)
REVERT: B  284 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7795 (tpp)
REVERT: B  338 ASP cc_start: 0.8642 (t0) cc_final: 0.8292 (t0)
REVERT: B  377 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7290 (t70)
REVERT: B  441 GLU cc_start: 0.7940 (pm20) cc_final: 0.7669 (pm20)
REVERT: B  563 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8618 (mtpp)
  outliers start: 14
  outliers final: 8
  residues processed: 129
  average time/residue: 1.2273
  time to fit residues: 166.2487
Evaluate side-chains
  131 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  213 ARG
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  379 ASP
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
A 572 HIS
B 197 ASN
B 366 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.119747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.106368 restraints weight = 9861.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.27
r_work: 0.3298 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6587  Z= 0.203
  Angle     :  0.543  17.563   8915  Z= 0.266
  Chirality :  0.039   0.138   1001
  Planarity :  0.003   0.035   1131
  Dihedral  :  3.572  15.311    868
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.29 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.30), residues: 775
  helix:  2.58 (0.28), residues: 323
  sheet: -0.02 (0.48), residues: 117
  loop :  0.04 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.005   0.001   HIS A 572 
 PHE   0.011   0.001   PHE A 253 
 TYR   0.019   0.001   TYR A 494 
 ARG   0.007   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7770 (mt) cc_final: 0.7276 (pp)
REVERT: A  237 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8325 (ptpp)
REVERT: A  261 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6822 (mm-40)
REVERT: A  282 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7454 (mtt90)
REVERT: A  384 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8259 (mtm110)
REVERT: A  395 LYS cc_start: 0.8815 (mttt) cc_final: 0.8576 (mtpm)
REVERT: A  440 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7035 (mp0)
REVERT: A  504 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7906 (mp10)
REVERT: A  543 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8207 (tm)
REVERT: A  563 LYS cc_start: 0.8524 (mttt) cc_final: 0.8111 (mmtm)
REVERT: B  174 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8283 (m-80)
REVERT: B  179 LYS cc_start: 0.7464 (tttt) cc_final: 0.7188 (tppt)
REVERT: B  213 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7615 (mtp180)
REVERT: B  284 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7820 (tpp)
REVERT: B  338 ASP cc_start: 0.8639 (t0) cc_final: 0.8285 (t0)
REVERT: B  377 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7085 (t0)
REVERT: B  441 GLU cc_start: 0.7883 (pm20) cc_final: 0.7595 (pm20)
REVERT: B  563 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8618 (mtpp)
  outliers start: 14
  outliers final: 7
  residues processed: 125
  average time/residue: 1.2608
  time to fit residues: 165.4365
Evaluate side-chains
  129 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  213 ARG
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 73 optimal weight:    0.4980
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0370
   chunk 78 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
A 572 HIS
B 197 ASN
B 339 ASN
B 366 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.107386 restraints weight = 9914.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.27
r_work: 0.3304 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6587  Z= 0.153
  Angle     :  0.535  17.448   8915  Z= 0.262
  Chirality :  0.039   0.139   1001
  Planarity :  0.003   0.033   1131
  Dihedral  :  3.531  15.314    868
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.02 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.30), residues: 775
  helix:  2.64 (0.28), residues: 323
  sheet: -0.02 (0.48), residues: 117
  loop :  0.07 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 505 
 HIS   0.004   0.001   HIS A 572 
 PHE   0.014   0.001   PHE A 228 
 TYR   0.021   0.001   TYR A 494 
 ARG   0.007   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7738 (mt) cc_final: 0.7185 (pp)
REVERT: A  235 ASP cc_start: 0.8120 (m-30) cc_final: 0.7875 (m-30)
REVERT: A  282 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7450 (mtt90)
REVERT: A  384 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8248 (mtm110)
REVERT: A  395 LYS cc_start: 0.8824 (mttt) cc_final: 0.8590 (mtpm)
REVERT: A  440 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6989 (mp0)
REVERT: A  504 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7900 (mp10)
REVERT: A  543 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8202 (tm)
REVERT: A  563 LYS cc_start: 0.8524 (mttt) cc_final: 0.8103 (mmtm)
REVERT: B  174 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8244 (m-80)
REVERT: B  179 LYS cc_start: 0.7403 (tttt) cc_final: 0.7132 (tppt)
REVERT: B  213 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7663 (mtp180)
REVERT: B  284 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7833 (tpp)
REVERT: B  338 ASP cc_start: 0.8601 (t0) cc_final: 0.8247 (t0)
REVERT: B  377 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7045 (t0)
REVERT: B  441 GLU cc_start: 0.7871 (pm20) cc_final: 0.7593 (pm20)
REVERT: B  563 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8624 (mtpp)
  outliers start: 14
  outliers final: 8
  residues processed: 125
  average time/residue: 1.2572
  time to fit residues: 165.1305
Evaluate side-chains
  131 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  213 ARG
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  339 ASN
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
A 572 HIS
B 197 ASN
B 366 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.120812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.107378 restraints weight = 10039.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.31
r_work: 0.3311 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.258   6587  Z= 0.386
  Angle     :  1.070  59.198   8915  Z= 0.663
  Chirality :  0.047   0.744   1001
  Planarity :  0.007   0.189   1131
  Dihedral  :  3.626  18.286    868
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.88 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.30), residues: 775
  helix:  2.63 (0.28), residues: 323
  sheet: -0.03 (0.48), residues: 117
  loop :  0.10 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.005   0.001   HIS A 572 
 PHE   0.011   0.001   PHE A 228 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 248 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5027.28 seconds
wall clock time: 86 minutes 24.99 seconds (5184.99 seconds total)