Starting phenix.real_space_refine
on Fri Oct 10 15:44:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wxj_37909/10_2025/8wxj_37909_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wxj_37909/10_2025/8wxj_37909.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wxj_37909/10_2025/8wxj_37909_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wxj_37909/10_2025/8wxj_37909_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wxj_37909/10_2025/8wxj_37909.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wxj_37909/10_2025/8wxj_37909.map"
  }
  resolution = 2.68
  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=   0.006
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      64      5.16       5
     C    4794      2.51       5
     N    1140      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 14 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: 7188
  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: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 9
          Unusual residues: {'SCN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 9
          Unusual residues: {'SCN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.95, per 1000 atoms: 0.27
  Number of scatterers: 7188
  At special positions: 0
  Unit cell: (73.15, 105.35, 69.65, 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      64     16.00
     O    1190      8.00
     N    1140      7.00
     C    4794      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 447.4 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 3 sheets defined
      75.3% alpha, 0.9% 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
      removed outlier: 3.585A  pdb=" N   ILE A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 183
      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 231 through 251
    Processing helix  chain 'A' and resid 263 through 280
    Processing helix  chain 'A' and resid 281 through 294
    Processing helix  chain 'A' and resid 299 through 324
    Processing helix  chain 'A' and resid 347 through 379
      removed outlier: 3.967A  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 449
      removed outlier: 3.571A  pdb=" N   SER A 446 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL A 448 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TRP A 449 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 475
      removed outlier: 3.527A  pdb=" N   TRP A 469 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 506
    Processing helix  chain 'A' and resid 520 through 537
    Processing helix  chain 'A' and resid 541 through 550
    Processing helix  chain 'A' and resid 555 through 574
    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 183
      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 231 through 251
    Processing helix  chain 'B' and resid 263 through 280
    Processing helix  chain 'B' and resid 281 through 294
    Processing helix  chain 'B' and resid 299 through 324
    Processing helix  chain 'B' and resid 347 through 379
      removed outlier: 3.967A  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 449
      removed outlier: 3.571A  pdb=" N   SER B 446 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL B 448 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TRP B 449 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 475
      removed outlier: 3.527A  pdb=" N   TRP B 469 " --> pdb=" O   VAL B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 506
    Processing helix  chain 'B' and resid 520 through 537
    Processing helix  chain 'B' and resid 541 through 550
    Processing helix  chain 'B' and resid 555 through 574
    Processing helix  chain 'B' and resid 576 through 585
    Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 298
    Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 511
    Processing sheet with id=AA3, first strand: chain 'B' and resid 510 through 511

    542 hydrogen bonds defined for protein.
    1614 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: 1.19

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1068
        1.28 -     1.42: 1966
        1.42 -     1.55: 4222
        1.55 -     1.68: 22
        1.68 -     1.81: 104
  Bond restraints: 7382
  Sorted by residual:
  bond pdb=" CA  PRO A 407 "
       pdb=" C   PRO A 407 "
    ideal  model  delta    sigma   weight residual
    1.517  1.538 -0.021 9.30e-03 1.16e+04 5.27e+00
  bond pdb=" CA  PRO B 407 "
       pdb=" C   PRO B 407 "
    ideal  model  delta    sigma   weight residual
    1.517  1.538 -0.021 9.30e-03 1.16e+04 5.27e+00
  bond pdb=" C   MET B 485 "
       pdb=" O   MET B 485 "
    ideal  model  delta    sigma   weight residual
    1.244  1.221  0.023 1.00e-02 1.00e+04 5.10e+00
  bond pdb=" C   MET A 485 "
       pdb=" O   MET A 485 "
    ideal  model  delta    sigma   weight residual
    1.244  1.221  0.023 1.00e-02 1.00e+04 5.10e+00
  bond pdb=" C   SCN A1003 "
       pdb=" S   SCN A1003 "
    ideal  model  delta    sigma   weight residual
    1.645  1.689 -0.044 2.00e-02 2.50e+03 4.77e+00
  ... (remaining 7377 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 9334
        1.96 -     3.92: 587
        3.92 -     5.89: 82
        5.89 -     7.85: 23
        7.85 -     9.81: 6
  Bond angle restraints: 10032
  Sorted by residual:
  angle pdb=" N   VAL A 269 "
        pdb=" CA  VAL A 269 "
        pdb=" C   VAL A 269 "
      ideal   model   delta    sigma   weight residual
     111.00  104.47    6.53 1.09e+00 8.42e-01 3.59e+01
  angle pdb=" N   PRO A 407 "
        pdb=" CA  PRO A 407 "
        pdb=" C   PRO A 407 "
      ideal   model   delta    sigma   weight residual
     110.70  117.26   -6.56 1.22e+00 6.72e-01 2.89e+01
  angle pdb=" N   PRO B 407 "
        pdb=" CA  PRO B 407 "
        pdb=" C   PRO B 407 "
      ideal   model   delta    sigma   weight residual
     110.70  117.26   -6.56 1.22e+00 6.72e-01 2.89e+01
  angle pdb=" CA  PHE A 512 "
        pdb=" C   PHE A 512 "
        pdb=" N   ASP A 513 "
      ideal   model   delta    sigma   weight residual
     119.56  116.89    2.67 5.80e-01 2.97e+00 2.11e+01
  angle pdb=" CA  PHE B 512 "
        pdb=" C   PHE B 512 "
        pdb=" N   ASP B 513 "
      ideal   model   delta    sigma   weight residual
     119.56  116.89    2.67 5.80e-01 2.97e+00 2.11e+01
  ... (remaining 10027 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 3418
       17.37 -    34.73: 423
       34.73 -    52.10: 287
       52.10 -    69.47: 118
       69.47 -    86.83: 6
  Dihedral angle restraints: 4252
    sinusoidal: 1586
      harmonic: 2666
  Sorted by residual:
  dihedral pdb=" C   PHE B 343 "
           pdb=" N   PHE B 343 "
           pdb=" CA  PHE B 343 "
           pdb=" CB  PHE B 343 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.17   10.57     0      2.50e+00 1.60e-01 1.79e+01
  dihedral pdb=" C   PHE A 343 "
           pdb=" N   PHE A 343 "
           pdb=" CA  PHE A 343 "
           pdb=" CB  PHE A 343 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.17   10.57     0      2.50e+00 1.60e-01 1.79e+01
  dihedral pdb=" N   PHE B 343 "
           pdb=" C   PHE B 343 "
           pdb=" CA  PHE B 343 "
           pdb=" CB  PHE B 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.25   -9.45     0      2.50e+00 1.60e-01 1.43e+01
  ... (remaining 4249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 924
       0.076 -    0.151: 196
       0.151 -    0.227: 36
       0.227 -    0.303: 8
       0.303 -    0.378: 6
  Chirality restraints: 1170
  Sorted by residual:
  chirality pdb=" CA  GLN B 154 "
            pdb=" N   GLN B 154 "
            pdb=" C   GLN B 154 "
            pdb=" CB  GLN B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.58e+00
  chirality pdb=" CA  GLN A 154 "
            pdb=" N   GLN A 154 "
            pdb=" C   GLN A 154 "
            pdb=" CB  GLN A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.58e+00
  chirality pdb=" CA  PHE B 343 "
            pdb=" N   PHE B 343 "
            pdb=" C   PHE B 343 "
            pdb=" CB  PHE B 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.39e+00
  ... (remaining 1167 not shown)

  Planarity restraints: 1226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 407 "    0.037 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO A 408 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 408 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 408 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 407 "    0.037 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO B 408 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 408 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 408 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 348 "   -0.036 5.00e-02 4.00e+02   5.49e-02 4.83e+00
        pdb=" N   PRO A 349 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 349 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 349 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1223 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1868
        2.77 -     3.30: 6954
        3.30 -     3.84: 13846
        3.84 -     4.37: 16809
        4.37 -     4.90: 26734
  Nonbonded interactions: 66211
  Sorted by model distance:
  nonbonded pdb=" O   THR A 550 "
            pdb=" CD1 ILE B 553 "
     model   vdw
     2.242 3.460
  nonbonded pdb=" CD1 ILE A 553 "
            pdb=" O   THR B 550 "
     model   vdw
     2.242 3.460
  nonbonded pdb=" CZ  PHE A 306 "
            pdb=" CE  MET B 560 "
     model   vdw
     2.334 3.760
  nonbonded pdb=" CE  MET A 560 "
            pdb=" CZ  PHE B 306 "
     model   vdw
     2.334 3.760
  nonbonded pdb=" OE2 GLU A 291 "
            pdb=" CE2 TYR B 302 "
     model   vdw
     2.363 3.340
  ... (remaining 66206 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: 0.02
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:             32.170
  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:          0.560
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.120
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3863
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      :  0.007   0.044   7382  Z= 0.514
  Angle     :  1.097   9.812  10032  Z= 0.749
  Chirality :  0.071   0.378   1170
  Planarity :  0.006   0.055   1226
  Dihedral  : 22.791  86.834   2544
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  1.51 %
    Allowed  :  7.13 %
    Favored  : 91.36 %
  Rotamer:
    Outliers : 31.50 %
    Allowed  : 11.81 %
    Favored  : 56.69 %
  Cbeta Deviations :  0.23 %
  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: -2.38 (0.25), residues: 926
  helix: -0.97 (0.18), residues: 686
  sheet:  None (None), residues: 0
  loop : -3.08 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 370 
 TYR   0.009   0.001   TYR B 578 
 PHE   0.019   0.002   PHE A 297 
 TRP   0.013   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00692 ( 7382)
  covalent geometry    : angle       1.09689 (10032)
  hydrogen bonds       : bond        0.14834 (  542)
  hydrogen bonds       : angle       6.45624 ( 1614)

*********************** 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
  407 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 240
    poor density    : 167
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5669 (mtp)
REVERT: A  283 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6074 (mp)
REVERT: A  294 SER cc_start: 0.5756 (t) cc_final: 0.5347 (p)
REVERT: A  419 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4687 (mmt)
REVERT: A  439 ASP cc_start: 0.4728 (t0) cc_final: 0.4504 (p0)
REVERT: B  250 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5663 (mtp)
REVERT: B  283 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6077 (mp)
REVERT: B  294 SER cc_start: 0.5791 (t) cc_final: 0.5305 (p)
REVERT: B  419 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4687 (mmt)
REVERT: B  439 ASP cc_start: 0.4724 (t0) cc_final: 0.4502 (p0)
  outliers start: 240
  outliers final: 48
  residues processed: 326
  average time/residue: 0.5173
  time to fit residues: 178.8104
Evaluate side-chains
  161 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 107
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  541 SER
Chi-restraints excluded: chain A residue  552 GLN
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  580 SER
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  250 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  384 GLN
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  419 MET
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  541 SER
Chi-restraints excluded: chain B residue  552 GLN
Chi-restraints excluded: chain B residue  553 ILE
Chi-restraints excluded: chain B residue  555 HIS
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:    0.7980
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
A 431 ASN
A 451 HIS
A 552 GLN
B 384 GLN
B 431 ASN
B 451 HIS
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.117290 restraints weight = 8183.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.00
r_work: 0.3236 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7382  Z= 0.152
  Angle     :  0.614   5.783  10032  Z= 0.324
  Chirality :  0.043   0.166   1170
  Planarity :  0.006   0.051   1226
  Dihedral  : 11.790  78.591   1078
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.89 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  8.92 %
    Allowed  : 24.28 %
    Favored  : 66.80 %
  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:  0.04 (0.27), residues: 926
  helix:  0.91 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -2.61 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 334 
 TYR   0.009   0.001   TYR B 578 
 PHE   0.010   0.002   PHE B 484 
 TRP   0.009   0.001   TRP A 303 
 HIS   0.001   0.001   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7382)
  covalent geometry    : angle       0.61405 (10032)
  hydrogen bonds       : bond        0.04536 (  542)
  hydrogen bonds       : angle       4.48449 ( 1614)

*********************** 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
  187 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 119
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 LYS cc_start: 0.7903 (tptt) cc_final: 0.7622 (tttm)
REVERT: A  248 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6370 (mttt)
REVERT: A  317 ARG cc_start: 0.6406 (mmt90) cc_final: 0.5781 (tpt170)
REVERT: B  204 LYS cc_start: 0.7913 (tptt) cc_final: 0.7626 (tttm)
REVERT: B  248 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6372 (mttt)
REVERT: B  317 ARG cc_start: 0.6432 (mmt90) cc_final: 0.5804 (tpt170)
  outliers start: 68
  outliers final: 32
  residues processed: 173
  average time/residue: 0.5541
  time to fit residues: 101.3626
Evaluate side-chains
  142 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  384 GLN
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  555 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 76 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 431 ASN
B 431 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.144073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.115769 restraints weight = 8205.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.99
r_work: 0.3251 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7382  Z= 0.149
  Angle     :  0.582   7.862  10032  Z= 0.301
  Chirality :  0.042   0.142   1170
  Planarity :  0.006   0.046   1226
  Dihedral  :  9.086  78.683   1030
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.54 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  8.79 %
    Allowed  : 23.49 %
    Favored  : 67.72 %
  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:  0.82 (0.27), residues: 926
  helix:  1.41 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -2.11 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 338 
 TYR   0.009   0.001   TYR A 578 
 PHE   0.022   0.001   PHE A 547 
 TRP   0.007   0.001   TRP A 303 
 HIS   0.002   0.001   HIS A 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7382)
  covalent geometry    : angle       0.58159 (10032)
  hydrogen bonds       : bond        0.04253 (  542)
  hydrogen bonds       : angle       4.25260 ( 1614)

*********************** 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
  179 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 112
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7504 (m)
REVERT: A  173 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7840 (mp)
REVERT: A  203 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6884 (mm)
REVERT: A  204 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7395 (tttm)
REVERT: A  248 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6496 (mttt)
REVERT: A  317 ARG cc_start: 0.6603 (mmt90) cc_final: 0.5967 (tpt170)
REVERT: A  334 ARG cc_start: 0.8031 (mpt180) cc_final: 0.7709 (mpt180)
REVERT: A  338 ARG cc_start: 0.6576 (mmp-170) cc_final: 0.6342 (mmt180)
REVERT: A  421 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7274 (mtt-85)
REVERT: A  425 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.8119 (m)
REVERT: A  431 ASN cc_start: 0.8172 (m-40) cc_final: 0.7907 (m110)
REVERT: B  139 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7489 (m)
REVERT: B  173 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7851 (mp)
REVERT: B  203 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6899 (mm)
REVERT: B  204 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7388 (tttm)
REVERT: B  248 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6486 (mttt)
REVERT: B  317 ARG cc_start: 0.6595 (mmt90) cc_final: 0.5968 (tpt170)
REVERT: B  334 ARG cc_start: 0.8008 (mpt180) cc_final: 0.7686 (mpt180)
REVERT: B  338 ARG cc_start: 0.6591 (mmp-170) cc_final: 0.6351 (mmt180)
REVERT: B  421 ARG cc_start: 0.7674 (mtm180) cc_final: 0.7302 (mtt-85)
REVERT: B  425 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8129 (m)
REVERT: B  431 ASN cc_start: 0.8151 (m-40) cc_final: 0.7886 (m110)
  outliers start: 67
  outliers final: 33
  residues processed: 157
  average time/residue: 0.5808
  time to fit residues: 96.2129
Evaluate side-chains
  151 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 106
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  392 LEU
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  139 SER
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  392 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.0470
   chunk 67 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 72 optimal weight:    0.4980
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 7 optimal weight:    0.3980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.144069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.115225 restraints weight = 8404.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.05
r_work: 0.3221 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7382  Z= 0.135
  Angle     :  0.561   8.115  10032  Z= 0.288
  Chirality :  0.042   0.140   1170
  Planarity :  0.005   0.049   1226
  Dihedral  :  8.210  77.429   1010
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.32 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 23.75 %
    Favored  : 68.64 %
  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:  1.20 (0.27), residues: 926
  helix:  1.68 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.94 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 370 
 TYR   0.009   0.001   TYR B 578 
 PHE   0.011   0.001   PHE B 547 
 TRP   0.006   0.001   TRP B 469 
 HIS   0.002   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7382)
  covalent geometry    : angle       0.56082 (10032)
  hydrogen bonds       : bond        0.04000 (  542)
  hydrogen bonds       : angle       4.13536 ( 1614)

*********************** 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
  167 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 109
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7470 (m)
REVERT: A  173 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7796 (mp)
REVERT: A  203 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6679 (mm)
REVERT: A  204 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7252 (tttm)
REVERT: A  248 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6344 (mttt)
REVERT: A  317 ARG cc_start: 0.6551 (mmt90) cc_final: 0.5951 (tpt170)
REVERT: A  431 ASN cc_start: 0.8131 (m-40) cc_final: 0.7728 (m110)
REVERT: A  515 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.6917 (tp)
REVERT: A  560 MET cc_start: 0.7844 (mmp) cc_final: 0.7178 (mtm)
REVERT: B  139 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7457 (m)
REVERT: B  173 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7822 (mp)
REVERT: B  203 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6669 (mm)
REVERT: B  204 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7243 (tttm)
REVERT: B  248 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6367 (mttt)
REVERT: B  317 ARG cc_start: 0.6560 (mmt90) cc_final: 0.5958 (tpt170)
REVERT: B  334 ARG cc_start: 0.7962 (mpt180) cc_final: 0.7708 (mpt180)
REVERT: B  431 ASN cc_start: 0.8116 (m-40) cc_final: 0.7715 (m110)
REVERT: B  515 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6924 (tp)
  outliers start: 58
  outliers final: 34
  residues processed: 151
  average time/residue: 0.5424
  time to fit residues: 86.9077
Evaluate side-chains
  144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 98
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  373 MET
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  555 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 57 optimal weight:    0.0770
   chunk 90 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.143453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.114640 restraints weight = 8340.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.06
r_work: 0.3219 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7382  Z= 0.140
  Angle     :  0.563   8.787  10032  Z= 0.288
  Chirality :  0.042   0.139   1170
  Planarity :  0.005   0.048   1226
  Dihedral  :  7.988  75.572   1008
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.43 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  8.01 %
    Allowed  : 23.36 %
    Favored  : 68.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.27), residues: 926
  helix:  1.82 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.78 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 370 
 TYR   0.009   0.001   TYR A 578 
 PHE   0.013   0.001   PHE A 306 
 TRP   0.006   0.001   TRP B 469 
 HIS   0.002   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7382)
  covalent geometry    : angle       0.56257 (10032)
  hydrogen bonds       : bond        0.03990 (  542)
  hydrogen bonds       : angle       4.07704 ( 1614)

*********************** 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
  160 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 99
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 SER cc_start: 0.7809 (OUTLIER) cc_final: 0.7471 (m)
REVERT: A  203 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6568 (mm)
REVERT: A  204 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7134 (tttm)
REVERT: A  248 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6409 (mttt)
REVERT: A  317 ARG cc_start: 0.6547 (mmt90) cc_final: 0.5938 (tpt170)
REVERT: A  334 ARG cc_start: 0.8006 (mpt180) cc_final: 0.7766 (mpt180)
REVERT: A  421 ARG cc_start: 0.7647 (mmm160) cc_final: 0.7283 (mtt-85)
REVERT: A  425 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8008 (m)
REVERT: A  431 ASN cc_start: 0.8145 (m-40) cc_final: 0.7710 (m110)
REVERT: A  515 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7126 (tp)
REVERT: A  560 MET cc_start: 0.7851 (mmp) cc_final: 0.7173 (mtm)
REVERT: B  139 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7453 (m)
REVERT: B  203 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6539 (mm)
REVERT: B  204 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7104 (tttm)
REVERT: B  248 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6446 (mttt)
REVERT: B  317 ARG cc_start: 0.6536 (mmt90) cc_final: 0.5952 (tpt170)
REVERT: B  334 ARG cc_start: 0.8003 (mpt180) cc_final: 0.7764 (mpt180)
REVERT: B  421 ARG cc_start: 0.7654 (mmm160) cc_final: 0.7283 (mtt-85)
REVERT: B  425 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8026 (m)
REVERT: B  431 ASN cc_start: 0.8126 (m-40) cc_final: 0.7697 (m110)
REVERT: B  515 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7130 (tp)
  outliers start: 61
  outliers final: 31
  residues processed: 141
  average time/residue: 0.5630
  time to fit residues: 84.1459
Evaluate side-chains
  135 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  392 LEU
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 A residue  555 HIS
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  204 LYS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  555 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 571 GLN
** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.141433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.112585 restraints weight = 8432.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.07
r_work: 0.3214 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7382  Z= 0.156
  Angle     :  0.573  10.113  10032  Z= 0.292
  Chirality :  0.043   0.139   1170
  Planarity :  0.005   0.047   1226
  Dihedral  :  7.607  71.928   1004
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.64 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  8.14 %
    Allowed  : 22.83 %
    Favored  : 69.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.52 (0.27), residues: 926
  helix:  1.88 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.72 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 304 
 TYR   0.009   0.001   TYR B 578 
 PHE   0.015   0.001   PHE A 306 
 TRP   0.006   0.001   TRP B 469 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7382)
  covalent geometry    : angle       0.57263 (10032)
  hydrogen bonds       : bond        0.04048 (  542)
  hydrogen bonds       : angle       4.09222 ( 1614)

*********************** 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
  156 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 94
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7541 (m)
REVERT: A  203 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6558 (mm)
REVERT: A  204 LYS cc_start: 0.7210 (tptt) cc_final: 0.6941 (tttm)
REVERT: A  248 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6502 (mttt)
REVERT: A  317 ARG cc_start: 0.6627 (mmt90) cc_final: 0.6004 (tpt170)
REVERT: A  334 ARG cc_start: 0.8056 (mpt180) cc_final: 0.7840 (mpt180)
REVERT: A  421 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7515 (mmm160)
REVERT: A  425 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8127 (m)
REVERT: A  431 ASN cc_start: 0.8231 (m-40) cc_final: 0.7947 (m110)
REVERT: A  560 MET cc_start: 0.8005 (mmp) cc_final: 0.7437 (mtm)
REVERT: B  139 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7535 (m)
REVERT: B  203 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6527 (mm)
REVERT: B  204 LYS cc_start: 0.7196 (tptt) cc_final: 0.6929 (tttm)
REVERT: B  248 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6537 (mttt)
REVERT: B  317 ARG cc_start: 0.6631 (mmt90) cc_final: 0.6036 (tpt170)
REVERT: B  334 ARG cc_start: 0.8078 (mpt180) cc_final: 0.7861 (mpt180)
REVERT: B  421 ARG cc_start: 0.7734 (mmm160) cc_final: 0.7504 (mmm160)
REVERT: B  425 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8129 (m)
REVERT: B  431 ASN cc_start: 0.8217 (m-40) cc_final: 0.7936 (m110)
  outliers start: 62
  outliers final: 29
  residues processed: 141
  average time/residue: 0.5521
  time to fit residues: 82.3787
Evaluate side-chains
  127 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 90
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  555 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0770
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.145227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.117333 restraints weight = 8365.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.04
r_work: 0.3313 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7382  Z= 0.136
  Angle     :  0.566  10.420  10032  Z= 0.286
  Chirality :  0.042   0.138   1170
  Planarity :  0.005   0.044   1226
  Dihedral  :  7.326  71.962   1002
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.32 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 24.67 %
    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:  1.69 (0.28), residues: 926
  helix:  1.96 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.52 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 304 
 TYR   0.010   0.001   TYR B 517 
 PHE   0.014   0.001   PHE A 306 
 TRP   0.006   0.001   TRP A 469 
 HIS   0.001   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7382)
  covalent geometry    : angle       0.56595 (10032)
  hydrogen bonds       : bond        0.03914 (  542)
  hydrogen bonds       : angle       4.03311 ( 1614)

*********************** 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
  139 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 89
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 SER cc_start: 0.7847 (OUTLIER) cc_final: 0.7527 (m)
REVERT: A  173 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7975 (mp)
REVERT: A  204 LYS cc_start: 0.7056 (tptt) cc_final: 0.6856 (tttm)
REVERT: A  248 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6582 (mttt)
REVERT: A  317 ARG cc_start: 0.6580 (mmt90) cc_final: 0.6021 (tpt170)
REVERT: A  334 ARG cc_start: 0.8092 (mpt180) cc_final: 0.7809 (mpt180)
REVERT: A  421 ARG cc_start: 0.7820 (mmm160) cc_final: 0.7602 (mmm160)
REVERT: A  425 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8199 (m)
REVERT: A  431 ASN cc_start: 0.8242 (m-40) cc_final: 0.7956 (m110)
REVERT: A  560 MET cc_start: 0.8097 (mmp) cc_final: 0.7366 (mtm)
REVERT: B  139 SER cc_start: 0.7887 (OUTLIER) cc_final: 0.7564 (m)
REVERT: B  173 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7961 (mp)
REVERT: B  248 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6608 (mttt)
REVERT: B  317 ARG cc_start: 0.6587 (mmt90) cc_final: 0.6051 (tpt170)
REVERT: B  334 ARG cc_start: 0.8115 (mpt180) cc_final: 0.7822 (mpt180)
REVERT: B  421 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7613 (mmm160)
REVERT: B  425 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8223 (m)
REVERT: B  431 ASN cc_start: 0.8234 (m-40) cc_final: 0.7939 (m110)
  outliers start: 50
  outliers final: 27
  residues processed: 124
  average time/residue: 0.6021
  time to fit residues: 78.5897
Evaluate side-chains
  120 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 85
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  373 MET
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  555 HIS
Chi-restraints excluded: chain B residue  564 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 68 optimal weight:    0.1980
   chunk 86 optimal weight:    2.9990
   chunk 85 optimal weight:    0.2980
   chunk 62 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0980
   chunk 43 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.145275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.117141 restraints weight = 8483.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.07
r_work: 0.3305 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7382  Z= 0.122
  Angle     :  0.560  10.509  10032  Z= 0.281
  Chirality :  0.042   0.138   1170
  Planarity :  0.005   0.044   1226
  Dihedral  :  6.837  72.618    995
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.54 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 25.33 %
    Favored  : 68.50 %
  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:  1.89 (0.28), residues: 926
  helix:  2.08 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.35 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 304 
 TYR   0.008   0.001   TYR B 578 
 PHE   0.017   0.001   PHE A 279 
 TRP   0.006   0.001   TRP B 469 
 HIS   0.001   0.000   HIS B 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7382)
  covalent geometry    : angle       0.55956 (10032)
  hydrogen bonds       : bond        0.03766 (  542)
  hydrogen bonds       : angle       3.97009 ( 1614)

*********************** 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
  137 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 90
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  139 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7521 (m)
REVERT: A  248 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6580 (mttt)
REVERT: A  317 ARG cc_start: 0.6591 (mmt90) cc_final: 0.6050 (tpt170)
REVERT: A  334 ARG cc_start: 0.8114 (mpt180) cc_final: 0.7856 (mpt180)
REVERT: A  421 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7602 (mmm160)
REVERT: A  425 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8195 (m)
REVERT: A  431 ASN cc_start: 0.8177 (m-40) cc_final: 0.7936 (m110)
REVERT: A  560 MET cc_start: 0.8072 (mmp) cc_final: 0.7383 (mtm)
REVERT: B  139 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7548 (m)
REVERT: B  248 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6588 (mttt)
REVERT: B  317 ARG cc_start: 0.6560 (mmt90) cc_final: 0.6050 (tpt170)
REVERT: B  334 ARG cc_start: 0.8131 (mpt180) cc_final: 0.7890 (mpt180)
REVERT: B  421 ARG cc_start: 0.7794 (mmm160) cc_final: 0.7589 (mmm160)
REVERT: B  425 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8183 (m)
REVERT: B  431 ASN cc_start: 0.8170 (m-40) cc_final: 0.7922 (m110)
REVERT: B  549 LEU cc_start: 0.7903 (mt) cc_final: 0.7651 (mp)
  outliers start: 47
  outliers final: 28
  residues processed: 120
  average time/residue: 0.6204
  time to fit residues: 78.5261
Evaluate side-chains
  121 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 87
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  373 MET
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  564 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0970
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0270
   chunk 47 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.145574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.117775 restraints weight = 8447.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.02
r_work: 0.3320 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7382  Z= 0.122
  Angle     :  0.563  10.510  10032  Z= 0.282
  Chirality :  0.042   0.139   1170
  Planarity :  0.005   0.043   1226
  Dihedral  :  6.775  72.861    995
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.00 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 26.12 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.28), residues: 926
  helix:  2.15 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.21 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 370 
 TYR   0.010   0.001   TYR B 206 
 PHE   0.024   0.001   PHE A 306 
 TRP   0.006   0.001   TRP B 469 
 HIS   0.002   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7382)
  covalent geometry    : angle       0.56271 (10032)
  hydrogen bonds       : bond        0.03730 (  542)
  hydrogen bonds       : angle       3.94409 ( 1614)

*********************** 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
  131 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 87
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7473 (m)
REVERT: A  248 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6589 (mttt)
REVERT: A  317 ARG cc_start: 0.6572 (mmt90) cc_final: 0.6045 (tpt170)
REVERT: A  334 ARG cc_start: 0.8097 (mpt180) cc_final: 0.7841 (mpt180)
REVERT: A  431 ASN cc_start: 0.8107 (m-40) cc_final: 0.7874 (m110)
REVERT: A  560 MET cc_start: 0.8030 (mmp) cc_final: 0.7325 (mtm)
REVERT: B  139 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7494 (m)
REVERT: B  248 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6569 (mttt)
REVERT: B  317 ARG cc_start: 0.6557 (mmt90) cc_final: 0.6070 (tpt170)
REVERT: B  334 ARG cc_start: 0.8106 (mpt180) cc_final: 0.7871 (mpt180)
REVERT: B  431 ASN cc_start: 0.8105 (m-40) cc_final: 0.7864 (m110)
REVERT: B  549 LEU cc_start: 0.7875 (mt) cc_final: 0.7622 (mp)
  outliers start: 44
  outliers final: 29
  residues processed: 117
  average time/residue: 0.6012
  time to fit residues: 74.2408
Evaluate side-chains
  115 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  555 HIS
Chi-restraints excluded: chain B residue  564 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0000
   chunk 12 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.145037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.116907 restraints weight = 8449.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.07
r_work: 0.3307 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7382  Z= 0.131
  Angle     :  0.573  10.282  10032  Z= 0.288
  Chirality :  0.042   0.138   1170
  Planarity :  0.005   0.043   1226
  Dihedral  :  6.736  71.960    995
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.10 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 26.64 %
    Favored  : 67.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.28), residues: 926
  helix:  2.16 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.21 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 304 
 TYR   0.011   0.001   TYR B 206 
 PHE   0.026   0.001   PHE A 306 
 TRP   0.005   0.001   TRP A 469 
 HIS   0.002   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7382)
  covalent geometry    : angle       0.57270 (10032)
  hydrogen bonds       : bond        0.03795 (  542)
  hydrogen bonds       : angle       3.96295 ( 1614)

********************** 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
  129 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 87
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7517 (m)
REVERT: A  248 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6615 (mttt)
REVERT: A  317 ARG cc_start: 0.6619 (mmt90) cc_final: 0.6087 (tpt170)
REVERT: A  334 ARG cc_start: 0.8098 (mpt180) cc_final: 0.7845 (mpt180)
REVERT: A  431 ASN cc_start: 0.8160 (m-40) cc_final: 0.7917 (m110)
REVERT: A  560 MET cc_start: 0.8086 (mmp) cc_final: 0.7422 (mtm)
REVERT: B  139 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7538 (m)
REVERT: B  248 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6594 (mttt)
REVERT: B  317 ARG cc_start: 0.6608 (mmt90) cc_final: 0.6107 (tpt170)
REVERT: B  334 ARG cc_start: 0.8115 (mpt180) cc_final: 0.7776 (mpt180)
REVERT: B  425 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8226 (m)
REVERT: B  431 ASN cc_start: 0.8155 (m-40) cc_final: 0.7904 (m110)
REVERT: B  549 LEU cc_start: 0.7917 (mt) cc_final: 0.7525 (mp)
  outliers start: 42
  outliers final: 28
  residues processed: 118
  average time/residue: 0.6189
  time to fit residues: 77.0074
Evaluate side-chains
  118 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ASN
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  248 LYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  336 ASN
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain B residue  377 ARG
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  425 SER
Chi-restraints excluded: chain B residue  443 LEU
Chi-restraints excluded: chain B residue  555 HIS
Chi-restraints excluded: chain B residue  564 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 91 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.144017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.115915 restraints weight = 8464.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.07
r_work: 0.3293 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7382  Z= 0.138
  Angle     :  0.584  10.023  10032  Z= 0.294
  Chirality :  0.043   0.141   1170
  Planarity :  0.005   0.044   1226
  Dihedral  :  6.688  70.200    995
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.21 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 26.77 %
    Favored  : 67.72 %
  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:  1.98 (0.28), residues: 926
  helix:  2.13 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.24 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 304 
 TYR   0.009   0.001   TYR A 206 
 PHE   0.028   0.001   PHE A 306 
 TRP   0.005   0.001   TRP B 322 
 HIS   0.002   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7382)
  covalent geometry    : angle       0.58388 (10032)
  hydrogen bonds       : bond        0.03888 (  542)
  hydrogen bonds       : angle       3.98652 ( 1614)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4077.25 seconds
wall clock time: 70 minutes 25.40 seconds (4225.40 seconds total)