Starting phenix.real_space_refine
on Fri Oct 10 15:44:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wxi_37908/10_2025/8wxi_37908_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wxi_37908/10_2025/8wxi_37908.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wxi_37908/10_2025/8wxi_37908.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wxi_37908/10_2025/8wxi_37908.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wxi_37908/10_2025/8wxi_37908_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wxi_37908/10_2025/8wxi_37908_neut.cif"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    4796      2.51       5
     N    1142      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7194
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 3585
          Classifications: {'peptide': 467}
          Link IDs: {'PTRANS': 24, 'TRANS': 442}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 3585
          Classifications: {'peptide': 467}
          Link IDs: {'PTRANS': 24, 'TRANS': 442}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 12
          Unusual residues: {'SCN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 12
          Unusual residues: {'SCN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.82, per 1000 atoms: 0.25
  Number of scatterers: 7194
  At special positions: 0
  Unit cell: (72.45, 107.45, 70.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1190      8.00
     N    1142      7.00
     C    4796      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=8, symmetry=0
  Number of additional bonds: simple=8, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 357.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 2 sheets defined
      74.0% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 115 through 153
    Processing helix  chain 'A' and resid 156 through 182
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 190 through 199
    Processing helix  chain 'A' and resid 208 through 224
    Processing helix  chain 'A' and resid 234 through 251
      removed outlier: 5.715A  pdb=" N   SER A 240 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 280
      removed outlier: 3.938A  pdb=" N   PHE A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 293
    Processing helix  chain 'A' and resid 298 through 323
    Processing helix  chain 'A' and resid 347 through 379
      removed outlier: 3.929A  pdb=" N   ARG A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
    Processing helix  chain 'A' and resid 391 through 405
    Processing helix  chain 'A' and resid 419 through 428
    Processing helix  chain 'A' and resid 443 through 448
      removed outlier: 3.823A  pdb=" N   VAL A 448 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 475
    Processing helix  chain 'A' and resid 483 through 506
    Processing helix  chain 'A' and resid 520 through 538
    Processing helix  chain 'A' and resid 541 through 551
    Processing helix  chain 'A' and resid 555 through 572
    Processing helix  chain 'A' and resid 576 through 585
    Processing helix  chain 'B' and resid 116 through 153
    Processing helix  chain 'B' and resid 156 through 182
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 208 through 224
    Processing helix  chain 'B' and resid 234 through 251
      removed outlier: 5.715A  pdb=" N   SER B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 280
      removed outlier: 3.938A  pdb=" N   PHE B 279 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 293
    Processing helix  chain 'B' and resid 298 through 323
    Processing helix  chain 'B' and resid 347 through 379
      removed outlier: 3.929A  pdb=" N   ARG B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 389
    Processing helix  chain 'B' and resid 391 through 405
    Processing helix  chain 'B' and resid 419 through 428
    Processing helix  chain 'B' and resid 443 through 448
      removed outlier: 3.823A  pdb=" N   VAL B 448 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 475
    Processing helix  chain 'B' and resid 483 through 506
    Processing helix  chain 'B' and resid 520 through 538
    Processing helix  chain 'B' and resid 541 through 551
    Processing helix  chain 'B' and resid 555 through 572
    Processing helix  chain 'B' and resid 576 through 585
    Processing sheet with id=AA1, first strand: chain 'A' and resid 510 through 511
    Processing sheet with id=AA2, first strand: chain 'B' and resid 510 through 511

    531 hydrogen bonds defined for protein.
    1575 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1070
        1.29 -     1.42: 1992
        1.42 -     1.55: 4169
        1.55 -     1.68: 49
        1.68 -     1.81: 106
  Bond restraints: 7386
  Sorted by residual:
  bond pdb=" C   SER B 183 "
       pdb=" N   PRO B 184 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 8.40e-03 1.42e+04 2.74e+01
  bond pdb=" C   SER A 183 "
       pdb=" N   PRO A 184 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 8.40e-03 1.42e+04 2.74e+01
  bond pdb=" C   PHE A 506 "
       pdb=" N   PRO A 507 "
    ideal  model  delta    sigma   weight residual
    1.335  1.379 -0.044 9.40e-03 1.13e+04 2.23e+01
  bond pdb=" C   PHE B 506 "
       pdb=" N   PRO B 507 "
    ideal  model  delta    sigma   weight residual
    1.335  1.379 -0.044 9.40e-03 1.13e+04 2.23e+01
  bond pdb=" CA  THR B 281 "
       pdb=" C   THR B 281 "
    ideal  model  delta    sigma   weight residual
    1.520  1.578 -0.058 1.25e-02 6.40e+03 2.16e+01
  ... (remaining 7381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.27: 9864
        4.27 -     8.54: 144
        8.54 -    12.81: 20
       12.81 -    17.08: 4
       17.08 -    21.35: 2
  Bond angle restraints: 10034
  Sorted by residual:
  angle pdb=" N   SER A 442 "
        pdb=" CA  SER A 442 "
        pdb=" C   SER A 442 "
      ideal   model   delta    sigma   weight residual
     114.12   99.92   14.20 1.39e+00 5.18e-01 1.04e+02
  angle pdb=" N   SER B 442 "
        pdb=" CA  SER B 442 "
        pdb=" C   SER B 442 "
      ideal   model   delta    sigma   weight residual
     114.12   99.92   14.20 1.39e+00 5.18e-01 1.04e+02
  angle pdb=" N   HIS B 237 "
        pdb=" CA  HIS B 237 "
        pdb=" C   HIS B 237 "
      ideal   model   delta    sigma   weight residual
     110.80   89.45   21.35 2.13e+00 2.20e-01 1.00e+02
  angle pdb=" N   HIS A 237 "
        pdb=" CA  HIS A 237 "
        pdb=" C   HIS A 237 "
      ideal   model   delta    sigma   weight residual
     110.80   89.45   21.35 2.13e+00 2.20e-01 1.00e+02
  angle pdb=" N   VAL A 236 "
        pdb=" CA  VAL A 236 "
        pdb=" CB  VAL A 236 "
      ideal   model   delta    sigma   weight residual
     111.23  127.11  -15.88 1.65e+00 3.67e-01 9.26e+01
  ... (remaining 10029 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.62: 3328
       15.62 -    31.24: 421
       31.24 -    46.86: 293
       46.86 -    62.49: 202
       62.49 -    78.11: 8
  Dihedral angle restraints: 4252
    sinusoidal: 1586
      harmonic: 2666
  Sorted by residual:
  dihedral pdb=" N   VAL A 236 "
           pdb=" C   VAL A 236 "
           pdb=" CA  VAL A 236 "
           pdb=" CB  VAL A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  145.63  -22.23     0      2.50e+00 1.60e-01 7.91e+01
  dihedral pdb=" N   VAL B 236 "
           pdb=" C   VAL B 236 "
           pdb=" CA  VAL B 236 "
           pdb=" CB  VAL B 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  145.63  -22.23     0      2.50e+00 1.60e-01 7.91e+01
  dihedral pdb=" C   VAL A 236 "
           pdb=" N   VAL A 236 "
           pdb=" CA  VAL A 236 "
           pdb=" CB  VAL A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -138.83   16.83     0      2.50e+00 1.60e-01 4.53e+01
  ... (remaining 4249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.133: 1025
       0.133 -    0.266: 123
       0.266 -    0.398: 12
       0.398 -    0.531: 4
       0.531 -    0.664: 6
  Chirality restraints: 1170
  Sorted by residual:
  chirality pdb=" CA  VAL A 236 "
            pdb=" N   VAL A 236 "
            pdb=" C   VAL A 236 "
            pdb=" CB  VAL A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.78    0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" CA  VAL B 236 "
            pdb=" N   VAL B 236 "
            pdb=" C   VAL B 236 "
            pdb=" CB  VAL B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.78    0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" CA  ASP B 429 "
            pdb=" N   ASP B 429 "
            pdb=" C   ASP B 429 "
            pdb=" CB  ASP B 429 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.90    0.61 2.00e-01 2.50e+01 9.34e+00
  ... (remaining 1167 not shown)

  Planarity restraints: 1226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 233 "   -0.047 5.00e-02 4.00e+02   7.23e-02 8.37e+00
        pdb=" N   PRO B 234 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B 234 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 234 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 233 "   -0.047 5.00e-02 4.00e+02   7.23e-02 8.37e+00
        pdb=" N   PRO A 234 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 407 "    0.043 5.00e-02 4.00e+02   6.50e-02 6.76e+00
        pdb=" N   PRO A 408 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 408 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 408 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1223 not shown)

  Histogram of nonbonded interaction distances:
        1.01 -     1.78: 15
        1.78 -     2.56: 54
        2.56 -     3.34: 9498
        3.34 -     4.12: 20736
        4.12 -     4.90: 36761
  Nonbonded interactions: 67064
  Sorted by model distance:
  nonbonded pdb=" CE1 PHE A 297 "
            pdb=" CE1 PHE B 297 "
     model   vdw
     1.006 3.640
  nonbonded pdb=" CZ  PHE A 297 "
            pdb=" CE1 PHE B 297 "
     model   vdw
     1.176 3.640
  nonbonded pdb=" CE1 PHE A 297 "
            pdb=" CZ  PHE B 297 "
     model   vdw
     1.176 3.640
  nonbonded pdb=" CE1 PHE A 297 "
            pdb=" CD1 PHE B 297 "
     model   vdw
     1.298 3.640
  nonbonded pdb=" CD1 PHE A 297 "
            pdb=" CE1 PHE B 297 "
     model   vdw
     1.298 3.640
  ... (remaining 67059 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             33.620
  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:          0.410
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.000
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3523
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      :  0.015   0.594   7394  Z= 1.368
  Angle     :  1.436  21.347  10034  Z= 0.946
  Chirality :  0.101   0.664   1170
  Planarity :  0.008   0.072   1226
  Dihedral  : 22.852  78.108   2544
  Min Nonbonded Distance : 1.006

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  7.56 %
    Favored  : 91.36 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 10.37 %
    Favored  : 56.30 %
  Cbeta Deviations :  0.70 %
  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: -3.44 (0.23), residues: 926
  helix: -1.69 (0.16), residues: 684
  sheet:  None (None), residues: 0
  loop : -3.62 (0.33), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 496 
 TYR   0.022   0.003   TYR A 206 
 PHE   0.021   0.003   PHE B 279 
 TRP   0.016   0.002   TRP B 469 
 HIS   0.007   0.001   HIS B 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00931 ( 7386)
  covalent geometry    : angle       1.43592 (10034)
  hydrogen bonds       : bond        0.14935 (  531)
  hydrogen bonds       : angle       6.73505 ( 1575)
  Misc. bond           : bond        0.36096 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  451 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 254
    poor density    : 197
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 ILE cc_start: 0.3790 (OUTLIER) cc_final: 0.3524 (mt)
REVERT: A  250 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.5003 (mtp)
REVERT: A  329 ILE cc_start: 0.4151 (OUTLIER) cc_final: 0.3672 (mp)
REVERT: A  332 LEU cc_start: 0.4039 (OUTLIER) cc_final: 0.3775 (pt)
REVERT: A  339 MET cc_start: 0.4855 (tpp) cc_final: 0.4136 (tpt)
REVERT: A  510 ILE cc_start: 0.4001 (OUTLIER) cc_final: 0.3756 (mt)
REVERT: A  515 ILE cc_start: 0.3854 (OUTLIER) cc_final: 0.3580 (mt)
REVERT: B  238 ILE cc_start: 0.3785 (OUTLIER) cc_final: 0.3521 (mt)
REVERT: B  250 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.4997 (mtp)
REVERT: B  264 SER cc_start: 0.4752 (OUTLIER) cc_final: 0.4316 (p)
REVERT: B  329 ILE cc_start: 0.4154 (OUTLIER) cc_final: 0.3674 (mp)
REVERT: B  332 LEU cc_start: 0.4039 (OUTLIER) cc_final: 0.3776 (pt)
REVERT: B  339 MET cc_start: 0.4859 (tpp) cc_final: 0.4141 (tpt)
REVERT: B  510 ILE cc_start: 0.3999 (OUTLIER) cc_final: 0.3753 (mt)
REVERT: B  515 ILE cc_start: 0.3854 (OUTLIER) cc_final: 0.3581 (mt)
  outliers start: 254
  outliers final: 44
  residues processed: 355
  average time/residue: 0.4192
  time to fit residues: 158.4336
Evaluate side-chains
  189 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 132
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 GLN
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  263 TYR
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  513 ASP
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  546 CYS
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  231 LYS
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  249 PHE
Chi-restraints excluded: chain B residue  250 MET
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  317 ARG
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  510 ILE
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  546 CYS
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  580 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.1980
   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 144 GLN
A 160 GLN
A 451 HIS
A 455 ASN
B 144 GLN
B 160 GLN
B 451 HIS
B 455 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.148703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.115429 restraints weight = 7484.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.95
r_work: 0.3254 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7394  Z= 0.179
  Angle     :  0.684   8.079  10034  Z= 0.368
  Chirality :  0.045   0.209   1170
  Planarity :  0.007   0.065   1226
  Dihedral  : 11.340  59.801   1099
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.46 %
    Favored  : 96.11 %
  Rotamer:
    Outliers : 11.15 %
    Allowed  : 20.08 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.26), residues: 926
  helix:  0.34 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -3.04 (0.36), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 199 
 TYR   0.010   0.001   TYR A 589 
 PHE   0.026   0.002   PHE A 341 
 TRP   0.011   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 7386)
  covalent geometry    : angle       0.68399 (10034)
  hydrogen bonds       : bond        0.04710 (  531)
  hydrogen bonds       : angle       4.75445 ( 1575)
  Misc. bond           : bond        0.00235 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 131
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  281 THR cc_start: 0.8270 (m) cc_final: 0.8036 (p)
REVERT: A  300 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6079 (ptt-90)
REVERT: A  332 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5908 (pt)
REVERT: A  338 ARG cc_start: 0.8352 (mtp180) cc_final: 0.8086 (mtt-85)
REVERT: A  385 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6455 (t80)
REVERT: A  421 ARG cc_start: 0.7966 (ptp-170) cc_final: 0.7417 (mtm110)
REVERT: A  439 ASP cc_start: 0.6368 (t70) cc_final: 0.6162 (p0)
REVERT: B  281 THR cc_start: 0.8258 (m) cc_final: 0.8022 (p)
REVERT: B  300 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6084 (ptt-90)
REVERT: B  332 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5881 (pt)
REVERT: B  385 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6453 (t80)
REVERT: B  421 ARG cc_start: 0.7984 (ptp-170) cc_final: 0.7438 (mtm110)
REVERT: B  439 ASP cc_start: 0.6357 (t70) cc_final: 0.6155 (p0)
  outliers start: 85
  outliers final: 23
  residues processed: 194
  average time/residue: 0.4158
  time to fit residues: 86.2424
Evaluate side-chains
  146 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 MET
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  263 TYR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain B residue  128 MET
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  515 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 59 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0970
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 180 HIS
B 180 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.145229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.111207 restraints weight = 7395.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.94
r_work: 0.3161 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7394  Z= 0.173
  Angle     :  0.652   6.827  10034  Z= 0.339
  Chirality :  0.043   0.152   1170
  Planarity :  0.006   0.052   1226
  Dihedral  :  7.352  53.488   1020
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.89 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  7.87 %
    Allowed  : 20.73 %
    Favored  : 71.39 %
  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:  0.45 (0.27), residues: 926
  helix:  1.31 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -2.75 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 199 
 TYR   0.008   0.001   TYR B 206 
 PHE   0.019   0.002   PHE A 343 
 TRP   0.011   0.001   TRP B 469 
 HIS   0.004   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 7386)
  covalent geometry    : angle       0.65205 (10034)
  hydrogen bonds       : bond        0.04414 (  531)
  hydrogen bonds       : angle       4.41289 ( 1575)
  Misc. bond           : bond        0.00212 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 128
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5325 (mt-10)
REVERT: A  290 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7729 (mt)
REVERT: A  300 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6346 (ptt-90)
REVERT: A  332 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6069 (pt)
REVERT: A  385 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6415 (t80)
REVERT: A  421 ARG cc_start: 0.8020 (ptp-170) cc_final: 0.7496 (mtm110)
REVERT: A  439 ASP cc_start: 0.6504 (t70) cc_final: 0.6275 (p0)
REVERT: B  123 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8390 (mm)
REVERT: B  290 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7728 (mt)
REVERT: B  300 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6323 (ptt-90)
REVERT: B  332 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6072 (pt)
REVERT: B  338 ARG cc_start: 0.8369 (mtp180) cc_final: 0.7970 (mtm180)
REVERT: B  385 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6411 (t80)
REVERT: B  421 ARG cc_start: 0.8019 (ptp-170) cc_final: 0.7496 (mtm110)
REVERT: B  439 ASP cc_start: 0.6507 (t70) cc_final: 0.6281 (p0)
REVERT: B  553 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7874 (mm)
  outliers start: 60
  outliers final: 22
  residues processed: 166
  average time/residue: 0.4857
  time to fit residues: 85.3797
Evaluate side-chains
  154 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  263 TYR
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  553 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.143543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.109269 restraints weight = 7505.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.98
r_work: 0.3131 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7394  Z= 0.170
  Angle     :  0.624   6.821  10034  Z= 0.323
  Chirality :  0.044   0.259   1170
  Planarity :  0.006   0.055   1226
  Dihedral  :  6.880  50.032   1016
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.10 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  8.14 %
    Allowed  : 21.92 %
    Favored  : 69.95 %
  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:  0.89 (0.27), residues: 926
  helix:  1.62 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -2.64 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 199 
 TYR   0.008   0.001   TYR A 206 
 PHE   0.015   0.002   PHE A 306 
 TRP   0.012   0.001   TRP B 469 
 HIS   0.002   0.001   HIS B 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 7386)
  covalent geometry    : angle       0.62436 (10034)
  hydrogen bonds       : bond        0.04275 (  531)
  hydrogen bonds       : angle       4.26486 ( 1575)
  Misc. bond           : bond        0.00216 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 128
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5355 (mt-10)
REVERT: A  152 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.6994 (mp10)
REVERT: A  262 TYR cc_start: 0.5012 (OUTLIER) cc_final: 0.3324 (p90)
REVERT: A  300 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6277 (ptt-90)
REVERT: A  332 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6138 (pt)
REVERT: A  338 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7070 (mmt-90)
REVERT: A  346 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8115 (mtmm)
REVERT: A  385 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6167 (t80)
REVERT: A  421 ARG cc_start: 0.8035 (ptp-170) cc_final: 0.7538 (mtm110)
REVERT: A  439 ASP cc_start: 0.6573 (t70) cc_final: 0.6322 (p0)
REVERT: A  511 LEU cc_start: 0.7734 (tp) cc_final: 0.7492 (tp)
REVERT: B  116 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5445 (mt-10)
REVERT: B  152 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7017 (mp10)
REVERT: B  300 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6319 (ptt-90)
REVERT: B  317 ARG cc_start: 0.6981 (mpt180) cc_final: 0.5787 (tmt-80)
REVERT: B  332 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6121 (pt)
REVERT: B  338 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7368 (mmt-90)
REVERT: B  345 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8485 (tt)
REVERT: B  346 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8105 (mtmm)
REVERT: B  385 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6165 (t80)
REVERT: B  421 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7531 (mtm110)
REVERT: B  439 ASP cc_start: 0.6583 (t70) cc_final: 0.6334 (p0)
REVERT: B  511 LEU cc_start: 0.7738 (tp) cc_final: 0.7498 (tp)
  outliers start: 62
  outliers final: 20
  residues processed: 173
  average time/residue: 0.5259
  time to fit residues: 95.9959
Evaluate side-chains
  156 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 121
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  152 GLN
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  263 TYR
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  338 ARG
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  550 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0670
   chunk 8 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.6920

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.145042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.111002 restraints weight = 7590.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.99
r_work: 0.3109 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.4678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7394  Z= 0.146
  Angle     :  0.604   6.529  10034  Z= 0.306
  Chirality :  0.044   0.288   1170
  Planarity :  0.005   0.053   1226
  Dihedral  :  6.629  51.573   1012
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.00 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  6.82 %
    Allowed  : 22.44 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.27), residues: 926
  helix:  1.82 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -2.57 (0.36), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 317 
 TYR   0.007   0.001   TYR A 206 
 PHE   0.016   0.001   PHE B 306 
 TRP   0.013   0.001   TRP B 469 
 HIS   0.002   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7386)
  covalent geometry    : angle       0.60377 (10034)
  hydrogen bonds       : bond        0.04043 (  531)
  hydrogen bonds       : angle       4.12837 ( 1575)
  Misc. bond           : bond        0.00237 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 133
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5514 (mt-10)
REVERT: A  204 LYS cc_start: 0.3773 (OUTLIER) cc_final: 0.3555 (ptmt)
REVERT: A  262 TYR cc_start: 0.5054 (OUTLIER) cc_final: 0.3419 (p90)
REVERT: A  300 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6247 (ptt-90)
REVERT: A  338 ARG cc_start: 0.8278 (mtt-85) cc_final: 0.7067 (mmt-90)
REVERT: A  346 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8116 (mtmm)
REVERT: A  385 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6070 (t80)
REVERT: A  421 ARG cc_start: 0.8013 (ptp-170) cc_final: 0.7519 (mtm110)
REVERT: A  439 ASP cc_start: 0.6608 (t70) cc_final: 0.6331 (p0)
REVERT: B  116 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5561 (mt-10)
REVERT: B  204 LYS cc_start: 0.3769 (OUTLIER) cc_final: 0.3555 (ptmt)
REVERT: B  300 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6260 (ptt-90)
REVERT: B  317 ARG cc_start: 0.6904 (mpt180) cc_final: 0.5726 (tmt-80)
REVERT: B  338 ARG cc_start: 0.8280 (mtp180) cc_final: 0.7369 (mmt-90)
REVERT: B  345 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (tp)
REVERT: B  346 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8104 (mtmm)
REVERT: B  385 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6066 (t80)
REVERT: B  421 ARG cc_start: 0.8003 (ptp-170) cc_final: 0.7512 (mtm110)
REVERT: B  439 ASP cc_start: 0.6609 (t70) cc_final: 0.6330 (p0)
  outliers start: 52
  outliers final: 21
  residues processed: 172
  average time/residue: 0.5364
  time to fit residues: 97.3996
Evaluate side-chains
  156 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  443 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 67 optimal weight:    0.2980
   chunk 64 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.144561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.110625 restraints weight = 7572.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.98
r_work: 0.3144 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.4810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7394  Z= 0.149
  Angle     :  0.609   6.651  10034  Z= 0.306
  Chirality :  0.044   0.309   1170
  Planarity :  0.005   0.052   1226
  Dihedral  :  6.061  51.161   1006
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.67 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 20.34 %
    Favored  : 72.05 %
  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:  1.43 (0.27), residues: 926
  helix:  2.09 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.56 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 304 
 TYR   0.007   0.001   TYR A 517 
 PHE   0.019   0.001   PHE A 306 
 TRP   0.013   0.001   TRP B 469 
 HIS   0.001   0.000   HIS B 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7386)
  covalent geometry    : angle       0.60872 (10034)
  hydrogen bonds       : bond        0.04046 (  531)
  hydrogen bonds       : angle       4.08334 ( 1575)
  Misc. bond           : bond        0.00241 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 124
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5907 (tt0)
REVERT: A  204 LYS cc_start: 0.3748 (OUTLIER) cc_final: 0.3527 (ptmt)
REVERT: A  262 TYR cc_start: 0.4950 (OUTLIER) cc_final: 0.3425 (p90)
REVERT: A  300 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6263 (ptt-90)
REVERT: A  338 ARG cc_start: 0.8272 (mtt-85) cc_final: 0.8026 (mtp85)
REVERT: A  346 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8108 (mtmm)
REVERT: A  385 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6110 (t80)
REVERT: A  421 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7500 (mtm110)
REVERT: A  439 ASP cc_start: 0.6650 (t70) cc_final: 0.6339 (p0)
REVERT: B  116 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5612 (mt-10)
REVERT: B  204 LYS cc_start: 0.3754 (OUTLIER) cc_final: 0.3542 (ptmt)
REVERT: B  300 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6212 (ptt-90)
REVERT: B  338 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7418 (mmt-90)
REVERT: B  345 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8450 (tp)
REVERT: B  346 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8074 (mtmm)
REVERT: B  385 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6104 (t80)
REVERT: B  421 ARG cc_start: 0.7980 (ptp-170) cc_final: 0.7492 (mtm110)
REVERT: B  439 ASP cc_start: 0.6652 (t70) cc_final: 0.6343 (p0)
  outliers start: 58
  outliers final: 24
  residues processed: 170
  average time/residue: 0.5507
  time to fit residues: 98.6469
Evaluate side-chains
  157 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  443 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 68 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.111549 restraints weight = 7535.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.98
r_work: 0.3119 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.4915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7394  Z= 0.142
  Angle     :  0.604   6.717  10034  Z= 0.304
  Chirality :  0.044   0.344   1170
  Planarity :  0.005   0.052   1226
  Dihedral  :  5.790  50.743   1004
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.89 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 21.65 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.27), residues: 926
  helix:  2.20 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.53 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 304 
 TYR   0.007   0.001   TYR A 206 
 PHE   0.019   0.001   PHE A 306 
 TRP   0.013   0.001   TRP B 469 
 HIS   0.001   0.000   HIS B 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7386)
  covalent geometry    : angle       0.60421 (10034)
  hydrogen bonds       : bond        0.03955 (  531)
  hydrogen bonds       : angle       4.04846 ( 1575)
  Misc. bond           : bond        0.00246 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 127
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ARG cc_start: 0.7528 (mtt90) cc_final: 0.7214 (mtp85)
REVERT: A  204 LYS cc_start: 0.3720 (OUTLIER) cc_final: 0.3462 (ptmm)
REVERT: A  300 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6273 (ptt-90)
REVERT: A  332 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6324 (pp)
REVERT: A  338 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8077 (mtt-85)
REVERT: A  346 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8046 (mtmm)
REVERT: A  385 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6059 (t80)
REVERT: A  421 ARG cc_start: 0.7986 (ptp-170) cc_final: 0.7497 (mtm110)
REVERT: A  439 ASP cc_start: 0.6694 (t70) cc_final: 0.6330 (p0)
REVERT: B  116 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5694 (mt-10)
REVERT: B  199 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7170 (mtp85)
REVERT: B  204 LYS cc_start: 0.3710 (OUTLIER) cc_final: 0.3460 (ptmm)
REVERT: B  262 TYR cc_start: 0.5048 (OUTLIER) cc_final: 0.3539 (p90)
REVERT: B  300 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6215 (ptt-90)
REVERT: B  317 ARG cc_start: 0.6964 (mpt180) cc_final: 0.5768 (tmt-80)
REVERT: B  332 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6323 (pp)
REVERT: B  338 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7439 (mmt-90)
REVERT: B  345 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8425 (tp)
REVERT: B  346 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8040 (mtmm)
REVERT: B  385 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6061 (t80)
REVERT: B  421 ARG cc_start: 0.7983 (ptp-170) cc_final: 0.7494 (mtm110)
REVERT: B  439 ASP cc_start: 0.6698 (t70) cc_final: 0.6329 (p0)
  outliers start: 49
  outliers final: 22
  residues processed: 164
  average time/residue: 0.5493
  time to fit residues: 94.8157
Evaluate side-chains
  157 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  338 ARG
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  443 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.145154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.111801 restraints weight = 7793.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.05
r_work: 0.3217 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7394  Z= 0.153
  Angle     :  0.612   6.845  10034  Z= 0.307
  Chirality :  0.044   0.307   1170
  Planarity :  0.006   0.052   1226
  Dihedral  :  5.816  50.967   1004
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.89 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 22.18 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.27), residues: 926
  helix:  2.23 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.47 (0.36), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 304 
 TYR   0.008   0.001   TYR A 206 
 PHE   0.020   0.002   PHE A 306 
 TRP   0.013   0.001   TRP B 469 
 HIS   0.001   0.000   HIS B 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7386)
  covalent geometry    : angle       0.61173 (10034)
  hydrogen bonds       : bond        0.04060 (  531)
  hydrogen bonds       : angle       4.07384 ( 1575)
  Misc. bond           : bond        0.00242 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 119
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5862 (tt0)
REVERT: A  204 LYS cc_start: 0.3717 (OUTLIER) cc_final: 0.3448 (ptmm)
REVERT: A  300 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6216 (ptt-90)
REVERT: A  332 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6213 (pp)
REVERT: A  338 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (mtt-85)
REVERT: A  346 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7992 (mtmm)
REVERT: A  385 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6086 (t80)
REVERT: A  421 ARG cc_start: 0.7887 (ptp-170) cc_final: 0.7405 (mtm110)
REVERT: A  439 ASP cc_start: 0.6652 (t70) cc_final: 0.6224 (p0)
REVERT: B  116 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5640 (mt-10)
REVERT: B  204 LYS cc_start: 0.3696 (OUTLIER) cc_final: 0.3432 (ptmm)
REVERT: B  300 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6184 (ptt-90)
REVERT: B  317 ARG cc_start: 0.6822 (mpt180) cc_final: 0.5637 (tmt-80)
REVERT: B  332 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6205 (pp)
REVERT: B  338 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7465 (mmt-90)
REVERT: B  345 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8317 (tt)
REVERT: B  346 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7964 (mtmm)
REVERT: B  385 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6072 (t80)
REVERT: B  421 ARG cc_start: 0.7890 (ptp-170) cc_final: 0.7407 (mtm110)
REVERT: B  439 ASP cc_start: 0.6655 (t70) cc_final: 0.6229 (p0)
  outliers start: 42
  outliers final: 22
  residues processed: 153
  average time/residue: 0.5666
  time to fit residues: 91.1705
Evaluate side-chains
  154 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 118
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  338 ARG
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  443 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    0.2980
   chunk 69 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0470
   chunk 38 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5478

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.146958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.113844 restraints weight = 7712.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.04
r_work: 0.3248 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.5254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7394  Z= 0.136
  Angle     :  0.600   7.037  10034  Z= 0.300
  Chirality :  0.044   0.300   1170
  Planarity :  0.005   0.052   1226
  Dihedral  :  5.711  50.824   1004
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.00 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 21.78 %
    Favored  : 72.70 %
  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:  1.81 (0.27), residues: 926
  helix:  2.35 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.37 (0.36), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 304 
 TYR   0.008   0.001   TYR A 206 
 PHE   0.022   0.001   PHE B 306 
 TRP   0.014   0.001   TRP B 469 
 HIS   0.001   0.000   HIS B 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7386)
  covalent geometry    : angle       0.59980 (10034)
  hydrogen bonds       : bond        0.03854 (  531)
  hydrogen bonds       : angle       4.01139 ( 1575)
  Misc. bond           : bond        0.00238 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 123
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5914 (tt0)
REVERT: A  199 ARG cc_start: 0.7535 (mtp85) cc_final: 0.7313 (mtp85)
REVERT: A  204 LYS cc_start: 0.3633 (OUTLIER) cc_final: 0.3416 (ptmm)
REVERT: A  300 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6216 (ptt-90)
REVERT: A  332 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6217 (pp)
REVERT: A  338 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7018 (mmt-90)
REVERT: A  346 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7964 (mtmm)
REVERT: A  385 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6034 (t80)
REVERT: A  421 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7371 (mtm110)
REVERT: A  439 ASP cc_start: 0.6708 (t70) cc_final: 0.6211 (p0)
REVERT: A  441 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7218 (pm20)
REVERT: B  116 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5893 (tt0)
REVERT: B  199 ARG cc_start: 0.7524 (mtp85) cc_final: 0.7291 (mtp85)
REVERT: B  204 LYS cc_start: 0.3623 (OUTLIER) cc_final: 0.3412 (ptmm)
REVERT: B  300 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6161 (ptt-90)
REVERT: B  317 ARG cc_start: 0.6781 (mpt180) cc_final: 0.5631 (tmt-80)
REVERT: B  332 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6231 (pp)
REVERT: B  338 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7334 (mmt-90)
REVERT: B  346 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7946 (mtmm)
REVERT: B  385 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6016 (t80)
REVERT: B  421 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7389 (mtm110)
REVERT: B  439 ASP cc_start: 0.6703 (t70) cc_final: 0.6208 (p0)
REVERT: B  441 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7215 (pm20)
  outliers start: 42
  outliers final: 23
  residues processed: 155
  average time/residue: 0.5871
  time to fit residues: 95.6863
Evaluate side-chains
  154 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  338 ARG
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  441 GLU
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  443 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0670
   chunk 65 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.7518

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

Flipped N/Q/H residues before XYZ refinement:
B 571 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.145773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.112623 restraints weight = 7700.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.04
r_work: 0.3229 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.5236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7394  Z= 0.149
  Angle     :  0.610   6.985  10034  Z= 0.305
  Chirality :  0.044   0.292   1170
  Planarity :  0.006   0.052   1226
  Dihedral  :  5.746  50.905   1004
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.10 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 22.31 %
    Favored  : 72.57 %
  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:  1.78 (0.27), residues: 926
  helix:  2.31 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.31 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 304 
 TYR   0.008   0.001   TYR A 206 
 PHE   0.024   0.002   PHE B 306 
 TRP   0.013   0.001   TRP B 469 
 HIS   0.001   0.000   HIS B 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7386)
  covalent geometry    : angle       0.60967 (10034)
  hydrogen bonds       : bond        0.03986 (  531)
  hydrogen bonds       : angle       4.04576 ( 1575)
  Misc. bond           : bond        0.00220 (    8)

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7291 (mtp85)
REVERT: A  204 LYS cc_start: 0.3653 (OUTLIER) cc_final: 0.3395 (ptmm)
REVERT: A  300 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6178 (ptt-90)
REVERT: A  332 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6197 (pp)
REVERT: A  338 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7093 (mmt-90)
REVERT: A  346 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7955 (mtmm)
REVERT: A  385 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6024 (t80)
REVERT: A  421 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7382 (mtm110)
REVERT: A  439 ASP cc_start: 0.6693 (t70) cc_final: 0.6165 (p0)
REVERT: B  116 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5899 (tt0)
REVERT: B  204 LYS cc_start: 0.3641 (OUTLIER) cc_final: 0.3428 (ptmm)
REVERT: B  300 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6200 (ptt-90)
REVERT: B  317 ARG cc_start: 0.6798 (mpt180) cc_final: 0.5639 (tmt-80)
REVERT: B  332 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6190 (pp)
REVERT: B  346 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7942 (mtmm)
REVERT: B  385 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6008 (t80)
REVERT: B  421 ARG cc_start: 0.7877 (ptp-170) cc_final: 0.7388 (mtm110)
REVERT: B  439 ASP cc_start: 0.6694 (t70) cc_final: 0.6168 (p0)
  outliers start: 39
  outliers final: 23
  residues processed: 148
  average time/residue: 0.6223
  time to fit residues: 96.5850
Evaluate side-chains
  150 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  279 PHE
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  338 ARG
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue  116 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  300 ARG
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  443 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 56 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 14 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 48 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.146911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.113798 restraints weight = 7738.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.04
r_work: 0.3241 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.5305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7394  Z= 0.138
  Angle     :  0.611   7.316  10034  Z= 0.306
  Chirality :  0.044   0.279   1170
  Planarity :  0.005   0.051   1226
  Dihedral  :  5.718  50.678   1004
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.21 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 22.83 %
    Favored  : 72.44 %
  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:  1.87 (0.27), residues: 926
  helix:  2.38 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.30 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 304 
 TYR   0.007   0.001   TYR A 206 
 PHE   0.024   0.001   PHE B 306 
 TRP   0.014   0.001   TRP B 469 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7386)
  covalent geometry    : angle       0.61063 (10034)
  hydrogen bonds       : bond        0.03850 (  531)
  hydrogen bonds       : angle       4.01721 ( 1575)
  Misc. bond           : bond        0.00203 (    8)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4121.37 seconds
wall clock time: 71 minutes 3.79 seconds (4263.79 seconds total)