Starting phenix.real_space_refine
on Fri Aug 22 17:26:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uyf_42804/08_2025/8uyf_42804.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uyf_42804/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uyf_42804/08_2025/8uyf_42804.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uyf_42804/08_2025/8uyf_42804.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uyf_42804/08_2025/8uyf_42804.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uyf_42804/08_2025/8uyf_42804.map"
  }
  resolution = 2.75
  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=   0.007 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'HIS:plan': 1, 'TPO:plan-1': 1, 'ARG: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: {'HIS:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 1.85, per 1000 atoms: 0.29
  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: 0.56
  Conformation dependent library (CDL) restraints added in 390.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.21
  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: 0.95

  Time building geometry restraints manager: 0.71 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:             1.250
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.920
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.110
-------------------------------------------------------------------------------
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= 0.173
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (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
 ARG   0.002   0.000   ARG B 374 
 TYR   0.008   0.001   TYR A 174 
 PHE   0.007   0.001   PHE A 253 
 TRP   0.005   0.001   TRP B 484 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6587)
  covalent geometry    : angle       0.51483 ( 8915)
  hydrogen bonds       : bond        0.23933 (  288)
  hydrogen bonds       : angle       6.45642 (  831)

*********************** 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  : 0.258 
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: 0.6397
  time to fit residues: 119.5690
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  : 0.271 
-------------------------------------------------------------------------------
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 49 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.117334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.103780 restraints weight = 9825.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.29
r_work: 0.3247 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6587  Z= 0.181
  Angle     :  0.551   5.485   8915  Z= 0.290
  Chirality :  0.041   0.140   1001
  Planarity :  0.004   0.034   1131
  Dihedral  :  4.176  39.116    870
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.30), residues: 775
  helix:  2.08 (0.28), residues: 328
  sheet: -0.17 (0.48), residues: 118
  loop :  0.13 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 248 
 TYR   0.014   0.002   TYR A 494 
 PHE   0.016   0.001   PHE A 452 
 TRP   0.006   0.001   TRP A 129 
 HIS   0.004   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 6587)
  covalent geometry    : angle       0.55088 ( 8915)
  hydrogen bonds       : bond        0.05637 (  288)
  hydrogen bonds       : angle       4.70505 (  831)

*********************** 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
  160 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  174 TYR cc_start: 0.8822 (m-80) cc_final: 0.8602 (m-80)
REVERT: A  178 LEU cc_start: 0.8090 (mt) cc_final: 0.7671 (pp)
REVERT: A  237 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8301 (ptpp)
REVERT: A  282 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7515 (mpt90)
REVERT: A  384 ARG cc_start: 0.8842 (mtp-110) cc_final: 0.8321 (mtm110)
REVERT: A  395 LYS cc_start: 0.8857 (mttt) cc_final: 0.8589 (mtpp)
REVERT: A  563 LYS cc_start: 0.8462 (mttt) cc_final: 0.8133 (mptt)
REVERT: B  133 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7721 (pp20)
REVERT: B  178 LEU cc_start: 0.7433 (mt) cc_final: 0.7200 (pt)
REVERT: B  179 LYS cc_start: 0.7886 (tttt) cc_final: 0.7543 (tppt)
REVERT: B  209 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8485 (mtmm)
REVERT: B  264 LYS cc_start: 0.7167 (mttt) cc_final: 0.6932 (mmmt)
REVERT: B  284 MET cc_start: 0.8480 (tpp) cc_final: 0.7849 (tpp)
REVERT: B  338 ASP cc_start: 0.8693 (t0) cc_final: 0.8359 (t0)
REVERT: B  366 GLN cc_start: 0.8844 (mt0) cc_final: 0.8298 (pt0)
REVERT: B  563 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8617 (mtpp)
  outliers start: 22
  outliers final: 11
  residues processed: 150
  average time/residue: 0.6099
  time to fit residues: 95.7607
Evaluate side-chains
  131 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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  229 ASN
Chi-restraints excluded: chain A residue  267 TYR
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  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 34 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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
B 504 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.119451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.105784 restraints weight = 9713.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.32
r_work: 0.3285 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2228

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= 0.113
  Angle     :  0.486   6.213   8915  Z= 0.252
  Chirality :  0.039   0.141   1001
  Planarity :  0.003   0.034   1131
  Dihedral  :  4.053  39.346    870
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.37 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.30), residues: 775
  helix:  2.32 (0.28), residues: 323
  sheet: -0.12 (0.48), residues: 117
  loop :  0.10 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 248 
 TYR   0.018   0.001   TYR A 494 
 PHE   0.011   0.001   PHE A 253 
 TRP   0.006   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6587)
  covalent geometry    : angle       0.48613 ( 8915)
  hydrogen bonds       : bond        0.04218 (  288)
  hydrogen bonds       : angle       4.27289 (  831)

*********************** 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
  146 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7971 (mt) cc_final: 0.7454 (pp)
REVERT: A  237 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8303 (ptpp)
REVERT: A  282 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7535 (mpt90)
REVERT: A  384 ARG cc_start: 0.8845 (mtp-110) cc_final: 0.8325 (mtm110)
REVERT: A  395 LYS cc_start: 0.8779 (mttt) cc_final: 0.8536 (mtpm)
REVERT: A  440 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7086 (mp0)
REVERT: A  504 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7856 (mp10)
REVERT: A  563 LYS cc_start: 0.8482 (mttt) cc_final: 0.8073 (mmtm)
REVERT: B  155 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7397 (p0)
REVERT: B  174 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8271 (m-80)
REVERT: B  178 LEU cc_start: 0.7408 (mt) cc_final: 0.7146 (pt)
REVERT: B  179 LYS cc_start: 0.7732 (tttt) cc_final: 0.7309 (tppt)
REVERT: B  209 LYS cc_start: 0.8684 (mmtp) cc_final: 0.8442 (mtmm)
REVERT: B  264 LYS cc_start: 0.7151 (mttt) cc_final: 0.6908 (mmmt)
REVERT: B  338 ASP cc_start: 0.8702 (t0) cc_final: 0.8334 (t0)
REVERT: B  366 GLN cc_start: 0.8841 (mt0) cc_final: 0.8525 (pt0)
REVERT: B  563 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8596 (mtpp)
  outliers start: 15
  outliers final: 4
  residues processed: 140
  average time/residue: 0.6649
  time to fit residues: 97.1789
Evaluate side-chains
  122 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  174 TYR
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 28 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 43 optimal weight:    0.3980
   chunk 66 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0582

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.118870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.105312 restraints weight = 9842.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.30
r_work: 0.3284 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6587  Z= 0.123
  Angle     :  0.501  10.564   8915  Z= 0.256
  Chirality :  0.039   0.140   1001
  Planarity :  0.003   0.034   1131
  Dihedral  :  3.761  14.725    868
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.50 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.30), residues: 775
  helix:  2.41 (0.28), residues: 323
  sheet: -0.09 (0.47), residues: 117
  loop :  0.05 (0.32), residues: 335

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6587)
  covalent geometry    : angle       0.50078 ( 8915)
  hydrogen bonds       : bond        0.04024 (  288)
  hydrogen bonds       : angle       4.16945 (  831)

*********************** 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
  138 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7954 (mt) cc_final: 0.7505 (pp)
REVERT: A  237 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8317 (ptpp)
REVERT: A  282 ARG cc_start: 0.8165 (mtp180) cc_final: 0.7561 (mpt90)
REVERT: A  384 ARG cc_start: 0.8883 (mtp-110) cc_final: 0.8446 (mtm110)
REVERT: A  395 LYS cc_start: 0.8834 (mttt) cc_final: 0.8590 (mtpm)
REVERT: A  440 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7088 (mp0)
REVERT: A  504 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7898 (mp10)
REVERT: A  543 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8175 (tm)
REVERT: A  563 LYS cc_start: 0.8518 (mttt) cc_final: 0.8107 (mmtm)
REVERT: B  155 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7417 (p0)
REVERT: B  174 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8271 (m-80)
REVERT: B  179 LYS cc_start: 0.7619 (tttt) cc_final: 0.7293 (tppt)
REVERT: B  209 LYS cc_start: 0.8639 (mmtp) cc_final: 0.8434 (mtmm)
REVERT: B  264 LYS cc_start: 0.7132 (mttt) cc_final: 0.6896 (mmmt)
REVERT: B  284 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7795 (tpp)
REVERT: B  338 ASP cc_start: 0.8695 (t0) cc_final: 0.8329 (t0)
REVERT: B  366 GLN cc_start: 0.8873 (mt0) cc_final: 0.8335 (pt0)
REVERT: B  563 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8588 (mtpp)
  outliers start: 18
  outliers final: 7
  residues processed: 129
  average time/residue: 0.6713
  time to fit residues: 90.3571
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  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  267 TYR
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  155 ASN
Chi-restraints excluded: chain B residue  161 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  488 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.0986

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.119326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.105975 restraints weight = 10001.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.28
r_work: 0.3278 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6587  Z= 0.124
  Angle     :  0.494   8.486   8915  Z= 0.252
  Chirality :  0.039   0.139   1001
  Planarity :  0.003   0.034   1131
  Dihedral  :  3.748  14.775    868
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.92 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.30), residues: 775
  helix:  2.47 (0.28), residues: 323
  sheet: -0.03 (0.47), residues: 117
  loop :  0.01 (0.32), residues: 335

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6587)
  covalent geometry    : angle       0.49388 ( 8915)
  hydrogen bonds       : bond        0.03907 (  288)
  hydrogen bonds       : angle       4.11922 (  831)

*********************** 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
  138 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7963 (mt) cc_final: 0.7528 (pp)
REVERT: A  237 LYS cc_start: 0.8590 (ptpt) cc_final: 0.8295 (ptpp)
REVERT: A  261 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6821 (mm-40)
REVERT: A  282 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7534 (mpt90)
REVERT: A  395 LYS cc_start: 0.8851 (mttt) cc_final: 0.8606 (mtpm)
REVERT: A  440 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7079 (mp0)
REVERT: A  504 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7890 (mp10)
REVERT: A  543 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8195 (tm)
REVERT: A  563 LYS cc_start: 0.8513 (mttt) cc_final: 0.8103 (mmtm)
REVERT: B  155 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7426 (p0)
REVERT: B  174 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8284 (m-80)
REVERT: B  179 LYS cc_start: 0.7574 (tttt) cc_final: 0.7208 (tppt)
REVERT: B  209 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8422 (mtmm)
REVERT: B  264 LYS cc_start: 0.7169 (mttt) cc_final: 0.6950 (mmmt)
REVERT: B  284 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7804 (tpp)
REVERT: B  338 ASP cc_start: 0.8676 (t0) cc_final: 0.8302 (t0)
REVERT: B  366 GLN cc_start: 0.8894 (mt0) cc_final: 0.8515 (pt0)
REVERT: B  441 GLU cc_start: 0.7926 (pm20) cc_final: 0.7688 (pm20)
REVERT: B  563 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8633 (mtpp)
  outliers start: 18
  outliers final: 8
  residues processed: 132
  average time/residue: 0.6545
  time to fit residues: 90.2775
Evaluate side-chains
  130 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  267 TYR
Chi-restraints excluded: chain A residue  407 SER
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  155 ASN
Chi-restraints excluded: chain B residue  161 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  488 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.117502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.104129 restraints weight = 9979.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.28
r_work: 0.3257 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6587  Z= 0.169
  Angle     :  0.541  15.764   8915  Z= 0.270
  Chirality :  0.040   0.138   1001
  Planarity :  0.004   0.034   1131
  Dihedral  :  3.865  15.265    868
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 14.92 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.30), residues: 775
  helix:  2.38 (0.28), residues: 323
  sheet:  0.03 (0.48), residues: 117
  loop : -0.10 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 248 
 TYR   0.020   0.001   TYR A 494 
 PHE   0.012   0.001   PHE A 452 
 TRP   0.006   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 6587)
  covalent geometry    : angle       0.54149 ( 8915)
  hydrogen bonds       : bond        0.04317 (  288)
  hydrogen bonds       : angle       4.20132 (  831)

*********************** 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
  142 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.8014 (mt) cc_final: 0.7642 (pp)
REVERT: A  261 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6770 (mm-40)
REVERT: A  282 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7539 (mpt90)
REVERT: A  395 LYS cc_start: 0.8847 (mttt) cc_final: 0.8599 (mtpm)
REVERT: A  440 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7085 (mp0)
REVERT: A  543 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8221 (tm)
REVERT: A  563 LYS cc_start: 0.8518 (mttt) cc_final: 0.8109 (mmtm)
REVERT: B  133 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7709 (mt-10)
REVERT: B  155 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.7414 (p0)
REVERT: B  174 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8248 (m-80)
REVERT: B  179 LYS cc_start: 0.7699 (tttt) cc_final: 0.7334 (tppt)
REVERT: B  264 LYS cc_start: 0.7176 (mttt) cc_final: 0.6959 (mmmt)
REVERT: B  284 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7833 (tpp)
REVERT: B  338 ASP cc_start: 0.8668 (t0) cc_final: 0.8279 (t0)
REVERT: B  366 GLN cc_start: 0.8944 (mt0) cc_final: 0.8375 (pt0)
REVERT: B  563 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8627 (mtpp)
  outliers start: 23
  outliers final: 13
  residues processed: 133
  average time/residue: 0.6444
  time to fit residues: 89.7119
Evaluate side-chains
  129 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  267 TYR
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  161 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  488 SER
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 19 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 197 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 = 0.3580 r_free = 0.3580 target = 0.119241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.105839 restraints weight = 9880.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.29
r_work: 0.3285 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.2572

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= 0.110
  Angle     :  0.537  17.095   8915  Z= 0.265
  Chirality :  0.039   0.140   1001
  Planarity :  0.003   0.032   1131
  Dihedral  :  3.722  15.287    868
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.88 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.30), residues: 775
  helix:  2.52 (0.28), residues: 323
  sheet:  0.02 (0.47), residues: 117
  loop : -0.03 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 248 
 TYR   0.021   0.001   TYR A 494 
 PHE   0.010   0.001   PHE A 253 
 TRP   0.005   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6587)
  covalent geometry    : angle       0.53687 ( 8915)
  hydrogen bonds       : bond        0.03651 (  288)
  hydrogen bonds       : angle       4.08156 (  831)

*********************** 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
  132 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.7973 (mt) cc_final: 0.7534 (pp)
REVERT: A  235 ASP cc_start: 0.8184 (m-30) cc_final: 0.7953 (m-30)
REVERT: A  282 ARG cc_start: 0.8139 (mtp180) cc_final: 0.7420 (mtt90)
REVERT: A  379 ASP cc_start: 0.8365 (p0) cc_final: 0.7824 (p0)
REVERT: A  395 LYS cc_start: 0.8839 (mttt) cc_final: 0.8600 (mtpm)
REVERT: A  440 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7069 (mp0)
REVERT: A  504 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7884 (mp10)
REVERT: A  543 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8205 (tm)
REVERT: A  563 LYS cc_start: 0.8508 (mttt) cc_final: 0.8103 (mmtm)
REVERT: B  174 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8266 (m-80)
REVERT: B  179 LYS cc_start: 0.7592 (tttt) cc_final: 0.7237 (tppt)
REVERT: B  264 LYS cc_start: 0.7175 (mttt) cc_final: 0.6956 (mmmt)
REVERT: B  284 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7866 (tpp)
REVERT: B  338 ASP cc_start: 0.8680 (t0) cc_final: 0.8283 (t0)
REVERT: B  366 GLN cc_start: 0.8920 (mt0) cc_final: 0.8361 (pt0)
REVERT: B  377 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7483 (t0)
REVERT: B  441 GLU cc_start: 0.7957 (pm20) cc_final: 0.7724 (pm20)
REVERT: B  480 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8398 (mm-40)
REVERT: B  563 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8600 (mtpp)
  outliers start: 16
  outliers final: 7
  residues processed: 125
  average time/residue: 0.6226
  time to fit residues: 81.5607
Evaluate side-chains
  125 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  407 SER
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 34 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 3 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0000
   chunk 54 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 229 ASN
B 197 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.119838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.106489 restraints weight = 9915.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.29
r_work: 0.3295 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6587  Z= 0.103
  Angle     :  0.534  17.142   8915  Z= 0.260
  Chirality :  0.039   0.140   1001
  Planarity :  0.003   0.032   1131
  Dihedral  :  3.652  15.212    868
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.15 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.30), residues: 775
  helix:  2.61 (0.28), residues: 323
  sheet:  0.02 (0.47), residues: 117
  loop : -0.01 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 248 
 TYR   0.021   0.001   TYR A 494 
 PHE   0.010   0.001   PHE A 253 
 TRP   0.007   0.001   TRP A 505 
 HIS   0.001   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 6587)
  covalent geometry    : angle       0.53429 ( 8915)
  hydrogen bonds       : bond        0.03435 (  288)
  hydrogen bonds       : angle       4.02568 (  831)

*********************** 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
  132 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.7919 (mt) cc_final: 0.7464 (pp)
REVERT: A  282 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7412 (mtt90)
REVERT: A  379 ASP cc_start: 0.8332 (p0) cc_final: 0.7799 (p0)
REVERT: A  384 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8338 (mtm110)
REVERT: A  395 LYS cc_start: 0.8825 (mttt) cc_final: 0.8581 (mtpm)
REVERT: A  440 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7051 (mp0)
REVERT: A  543 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8216 (tm)
REVERT: A  563 LYS cc_start: 0.8503 (mttt) cc_final: 0.8087 (mmtm)
REVERT: B  174 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8289 (m-80)
REVERT: B  179 LYS cc_start: 0.7453 (tttt) cc_final: 0.7075 (tppt)
REVERT: B  264 LYS cc_start: 0.7156 (mttt) cc_final: 0.6937 (mmmt)
REVERT: B  284 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7847 (tpp)
REVERT: B  338 ASP cc_start: 0.8674 (t0) cc_final: 0.8293 (t0)
REVERT: B  366 GLN cc_start: 0.8915 (mt0) cc_final: 0.8524 (pt0)
REVERT: B  377 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7471 (t70)
REVERT: B  441 GLU cc_start: 0.7912 (pm20) cc_final: 0.7646 (pm20)
REVERT: B  563 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8596 (mtpp)
  outliers start: 14
  outliers final: 7
  residues processed: 125
  average time/residue: 0.6293
  time to fit residues: 82.3614
Evaluate side-chains
  124 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  407 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0050
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 229 ASN
B 197 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.120272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.106989 restraints weight = 10005.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.29
r_work: 0.3306 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6587  Z= 0.105
  Angle     :  0.553  17.441   8915  Z= 0.268
  Chirality :  0.039   0.140   1001
  Planarity :  0.003   0.032   1131
  Dihedral  :  3.595  15.307    868
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.30), residues: 775
  helix:  2.64 (0.28), residues: 323
  sheet:  0.05 (0.47), residues: 117
  loop :  0.02 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 248 
 TYR   0.019   0.001   TYR A 494 
 PHE   0.010   0.001   PHE A 253 
 TRP   0.009   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6587)
  covalent geometry    : angle       0.55322 ( 8915)
  hydrogen bonds       : bond        0.03313 (  288)
  hydrogen bonds       : angle       4.01736 (  831)

*********************** 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
  129 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 TYR cc_start: 0.8842 (m-80) cc_final: 0.8636 (m-80)
REVERT: A  178 LEU cc_start: 0.7825 (mt) cc_final: 0.7325 (pp)
REVERT: A  282 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7407 (mtt90)
REVERT: A  376 GLU cc_start: 0.8269 (mp0) cc_final: 0.8014 (mp0)
REVERT: A  384 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8393 (mtm110)
REVERT: A  395 LYS cc_start: 0.8818 (mttt) cc_final: 0.8570 (mtpm)
REVERT: A  440 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7041 (mp0)
REVERT: A  504 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7881 (mp10)
REVERT: A  543 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8218 (tm)
REVERT: A  563 LYS cc_start: 0.8483 (mttt) cc_final: 0.8064 (mmtm)
REVERT: B  174 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8281 (m-80)
REVERT: B  179 LYS cc_start: 0.7355 (tttt) cc_final: 0.7045 (tppt)
REVERT: B  264 LYS cc_start: 0.7153 (mttt) cc_final: 0.6927 (mmmt)
REVERT: B  284 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7841 (tpp)
REVERT: B  338 ASP cc_start: 0.8668 (t0) cc_final: 0.8277 (t0)
REVERT: B  366 GLN cc_start: 0.8921 (mt0) cc_final: 0.8329 (pt0)
REVERT: B  377 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7139 (t0)
REVERT: B  563 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8584 (mtpp)
  outliers start: 13
  outliers final: 7
  residues processed: 123
  average time/residue: 0.6432
  time to fit residues: 82.8281
Evaluate side-chains
  123 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
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  379 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 1 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 229 ASN
B 197 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.118896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.105577 restraints weight = 9859.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.28
r_work: 0.3282 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6587  Z= 0.138
  Angle     :  0.573  17.938   8915  Z= 0.279
  Chirality :  0.039   0.139   1001
  Planarity :  0.003   0.033   1131
  Dihedral  :  3.672  15.316    868
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.71 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.30), residues: 775
  helix:  2.56 (0.28), residues: 323
  sheet:  0.06 (0.47), residues: 117
  loop : -0.02 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 248 
 TYR   0.019   0.001   TYR A 494 
 PHE   0.011   0.001   PHE A 253 
 TRP   0.007   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6587)
  covalent geometry    : angle       0.57318 ( 8915)
  hydrogen bonds       : bond        0.03677 (  288)
  hydrogen bonds       : angle       4.09881 (  831)

********************** 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
  126 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.7863 (mt) cc_final: 0.7435 (pp)
REVERT: A  282 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7440 (mtt90)
REVERT: A  384 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8423 (mtm110)
REVERT: A  395 LYS cc_start: 0.8835 (mttt) cc_final: 0.8587 (mtpm)
REVERT: A  440 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7016 (mp0)
REVERT: A  543 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8239 (tm)
REVERT: A  563 LYS cc_start: 0.8517 (mttt) cc_final: 0.8100 (mmtm)
REVERT: B  174 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8270 (m-80)
REVERT: B  179 LYS cc_start: 0.7442 (tttt) cc_final: 0.7175 (tppt)
REVERT: B  264 LYS cc_start: 0.7178 (mttt) cc_final: 0.6942 (mmmt)
REVERT: B  338 ASP cc_start: 0.8677 (t0) cc_final: 0.8266 (t0)
REVERT: B  366 GLN cc_start: 0.8929 (mt0) cc_final: 0.8355 (pt0)
REVERT: B  377 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7105 (t0)
REVERT: B  563 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8627 (mtpp)
  outliers start: 14
  outliers final: 9
  residues processed: 120
  average time/residue: 0.6410
  time to fit residues: 80.5243
Evaluate side-chains
  121 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0970
   chunk 43 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 12 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 229 ASN
B 197 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.119575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.106280 restraints weight = 9883.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.27
r_work: 0.3294 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6587  Z= 0.114
  Angle     :  0.565  17.628   8915  Z= 0.275
  Chirality :  0.039   0.139   1001
  Planarity :  0.003   0.032   1131
  Dihedral  :  3.642  15.312    868
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.43 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.30), residues: 775
  helix:  2.63 (0.29), residues: 323
  sheet:  0.06 (0.47), residues: 117
  loop :  0.04 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 248 
 TYR   0.021   0.001   TYR A 494 
 PHE   0.010   0.001   PHE A 253 
 TRP   0.008   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6587)
  covalent geometry    : angle       0.56473 ( 8915)
  hydrogen bonds       : bond        0.03461 (  288)
  hydrogen bonds       : angle       4.04612 (  831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2669.17 seconds
wall clock time: 46 minutes 22.15 seconds (2782.15 seconds total)