Starting phenix.real_space_refine
on Tue Feb 11 20:36:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6l48_0832/02_2025/6l48_0832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l48_0832/02_2025/6l48_0832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6l48_0832/02_2025/6l48_0832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l48_0832/02_2025/6l48_0832.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l48_0832/02_2025/6l48_0832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l48_0832/02_2025/6l48_0832.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      36      5.16       5
     C    4482      2.51       5
     N    1000      2.21       5
     O    1010      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6528
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3236
          Classifications: {'peptide': 397}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 17, 'TRANS': 379}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 139
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 123
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 104
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.09, per 1000 atoms: 0.78
  Number of scatterers: 6528
  At special positions: 0
  Unit cell: (141.075, 74.195, 72.105, 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      36     16.00
     O    1010      8.00
     N    1000      7.00
     C    4482      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 938.6 milliseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1532

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      81.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 127 through 133
      removed outlier: 3.552A  pdb=" N   GLU A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 165
    Processing helix  chain 'A' and resid 171 through 178
      removed outlier: 3.625A  pdb=" N   SER A 175 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 213
      Proline residue:  A 199  - end of helix
      removed outlier: 4.113A  pdb=" N   THR A 208 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLY A 209 " --> pdb=" O   HIS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
      removed outlier: 4.116A  pdb=" N   ARG A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU A 221 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 247
      Proline residue:  A 239  - end of helix
      removed outlier: 3.702A  pdb=" N   VAL A 243 " --> pdb=" O   PRO A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 284
      removed outlier: 3.858A  pdb=" N   ILE A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      Proline residue:  A 276  - end of helix
    Processing helix  chain 'A' and resid 293 through 301
    Processing helix  chain 'A' and resid 319 through 344
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.521A  pdb=" N   PHE A 349 " --> pdb=" O   CYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 369
    Processing helix  chain 'A' and resid 369 through 395
    Processing helix  chain 'A' and resid 412 through 418
      removed outlier: 3.782A  pdb=" N   ARG A 418 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 439
    Processing helix  chain 'A' and resid 444 through 469
      removed outlier: 4.030A  pdb=" N   ALA A 448 " --> pdb=" O   PHE A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 487
      removed outlier: 3.672A  pdb=" N   PHE A 486 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 526
    Processing helix  chain 'B' and resid 127 through 133
      removed outlier: 3.552A  pdb=" N   GLU B 131 " --> pdb=" O   SER B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 165
    Processing helix  chain 'B' and resid 171 through 178
      removed outlier: 3.625A  pdb=" N   SER B 175 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 213
      Proline residue:  B 199  - end of helix
      removed outlier: 4.113A  pdb=" N   THR B 208 " --> pdb=" O   GLN B 204 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLY B 209 " --> pdb=" O   HIS B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 232
      removed outlier: 4.116A  pdb=" N   ARG B 219 " --> pdb=" O   HIS B 215 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU B 221 " --> pdb=" O   LEU B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 247
      Proline residue:  B 239  - end of helix
      removed outlier: 3.701A  pdb=" N   VAL B 243 " --> pdb=" O   PRO B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 284
      removed outlier: 3.858A  pdb=" N   ILE B 256 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
      Proline residue:  B 276  - end of helix
    Processing helix  chain 'B' and resid 293 through 301
    Processing helix  chain 'B' and resid 319 through 344
    Processing helix  chain 'B' and resid 345 through 350
      removed outlier: 3.520A  pdb=" N   PHE B 349 " --> pdb=" O   CYS B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 369
    Processing helix  chain 'B' and resid 369 through 395
    Processing helix  chain 'B' and resid 412 through 418
      removed outlier: 3.781A  pdb=" N   ARG B 418 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 439
    Processing helix  chain 'B' and resid 444 through 469
      removed outlier: 4.029A  pdb=" N   ALA B 448 " --> pdb=" O   PHE B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 487
      removed outlier: 3.672A  pdb=" N   PHE B 486 " --> pdb=" O   PHE B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 526

    472 hydrogen bonds defined for protein.
    1416 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: 1.88

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1831
        1.34 -     1.46: 2056
        1.46 -     1.58: 2835
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6780
  Sorted by residual:
  bond pdb=" CA  ARG B 309 "
       pdb=" C   ARG B 309 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.027 1.30e-02 5.92e+03 4.39e+00
  bond pdb=" CA  ARG A 309 "
       pdb=" C   ARG A 309 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.30e-02 5.92e+03 4.38e+00
  bond pdb=" C13 CLR B2001 "
       pdb=" C14 CLR B2001 "
    ideal  model  delta    sigma   weight residual
    1.537  1.509  0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C13 CLR A2001 "
       pdb=" C14 CLR A2001 "
    ideal  model  delta    sigma   weight residual
    1.537  1.510  0.027 2.00e-02 2.50e+03 1.87e+00
  bond pdb=" N   ASP A 310 "
       pdb=" CA  ASP A 310 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.64e+00
  ... (remaining 6775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 9011
        1.90 -     3.80: 194
        3.80 -     5.69: 47
        5.69 -     7.59: 10
        7.59 -     9.49: 10
  Bond angle restraints: 9272
  Sorted by residual:
  angle pdb=" N   ARG B 309 "
        pdb=" CA  ARG B 309 "
        pdb=" C   ARG B 309 "
      ideal   model   delta    sigma   weight residual
     111.28  104.58    6.70 1.09e+00 8.42e-01 3.78e+01
  angle pdb=" N   ARG A 309 "
        pdb=" CA  ARG A 309 "
        pdb=" C   ARG A 309 "
      ideal   model   delta    sigma   weight residual
     111.28  104.59    6.69 1.09e+00 8.42e-01 3.76e+01
  angle pdb=" C   TRP A 388 "
        pdb=" N   LEU A 389 "
        pdb=" CA  LEU A 389 "
      ideal   model   delta    sigma   weight residual
     122.38  113.90    8.48 1.81e+00 3.05e-01 2.19e+01
  angle pdb=" C   TRP B 388 "
        pdb=" N   LEU B 389 "
        pdb=" CA  LEU B 389 "
      ideal   model   delta    sigma   weight residual
     122.38  113.92    8.46 1.81e+00 3.05e-01 2.19e+01
  angle pdb=" N   ASP A 310 "
        pdb=" CA  ASP A 310 "
        pdb=" C   ASP A 310 "
      ideal   model   delta    sigma   weight residual
     110.80  119.11   -8.31 2.13e+00 2.20e-01 1.52e+01
  ... (remaining 9267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.42: 3462
       14.42 -    28.84: 297
       28.84 -    43.26: 85
       43.26 -    57.67: 10
       57.67 -    72.09: 2
  Dihedral angle restraints: 3856
    sinusoidal: 1482
      harmonic: 2374
  Sorted by residual:
  dihedral pdb=" N   ASP A 310 "
           pdb=" C   ASP A 310 "
           pdb=" CA  ASP A 310 "
           pdb=" CB  ASP A 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.29  -11.49     0      2.50e+00 1.60e-01 2.11e+01
  dihedral pdb=" N   ASP B 310 "
           pdb=" C   ASP B 310 "
           pdb=" CA  ASP B 310 "
           pdb=" CB  ASP B 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.29  -11.49     0      2.50e+00 1.60e-01 2.11e+01
  dihedral pdb=" CA  GLN A 354 "
           pdb=" C   GLN A 354 "
           pdb=" N   GLU A 355 "
           pdb=" CA  GLU A 355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.66  -22.34     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 3853 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 988
       0.100 -    0.201: 30
       0.201 -    0.301: 2
       0.301 -    0.401: 0
       0.401 -    0.502: 2
  Chirality restraints: 1022
  Sorted by residual:
  chirality pdb=" CA  ASP A 310 "
            pdb=" N   ASP A 310 "
            pdb=" C   ASP A 310 "
            pdb=" CB  ASP A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.29e+00
  chirality pdb=" CA  ASP B 310 "
            pdb=" N   ASP B 310 "
            pdb=" C   ASP B 310 "
            pdb=" CB  ASP B 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.28e+00
  chirality pdb=" CA  ARG B 309 "
            pdb=" N   ARG B 309 "
            pdb=" C   ARG B 309 "
            pdb=" CB  ARG B 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1019 not shown)

  Planarity restraints: 1100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 308 "   -0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   TYR B 308 "    0.069 2.00e-02 2.50e+03
        pdb=" O   TYR B 308 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ARG B 309 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 308 "    0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   TYR A 308 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   TYR A 308 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ARG A 309 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 389 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.06e+00
        pdb=" C   LEU A 389 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   LEU A 389 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ASN A 390 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1097 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 848
        2.75 -     3.29: 6781
        3.29 -     3.83: 11195
        3.83 -     4.36: 12372
        4.36 -     4.90: 21540
  Nonbonded interactions: 52736
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 130 "
            pdb=" OH  TYR B 322 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OD2 ASP A 130 "
            pdb=" OH  TYR A 322 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OH  TYR B 299 "
            pdb=" O   LEU B 396 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR A 299 "
            pdb=" O   LEU A 396 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   PHE A 237 "
            pdb=" N   TYR A 241 "
     model   vdw
     2.284 3.120
  ... (remaining 52731 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: 0.03
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.410
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.520
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6780  Z= 0.212
  Angle     :  0.762   9.490   9272  Z= 0.404
  Chirality :  0.050   0.502   1022
  Planarity :  0.006   0.040   1100
  Dihedral  : 12.004  72.093   2324
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  7.34 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.26), residues: 782
  helix: -1.58 (0.18), residues: 600
  sheet:  None (None), residues: 0
  loop : -4.04 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 504 
 HIS   0.008   0.001   HIS A 425 
 PHE   0.015   0.001   PHE A 331 
 TYR   0.013   0.001   TYR B 433 
 ARG   0.003   0.000   ARG B 350 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 217
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.7028 (pmt170) cc_final: 0.6720 (ptt-90)
REVERT: A  151 LEU cc_start: 0.8834 (tt) cc_final: 0.8447 (mt)
REVERT: A  205 HIS cc_start: 0.8220 (t70) cc_final: 0.7766 (t-170)
REVERT: A  241 TYR cc_start: 0.7991 (t80) cc_final: 0.7616 (t80)
REVERT: A  246 TYR cc_start: 0.8110 (m-10) cc_final: 0.7796 (m-80)
REVERT: A  273 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7002 (tm-30)
REVERT: A  293 THR cc_start: 0.8402 (p) cc_final: 0.7688 (t)
REVERT: A  468 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7697 (mm)
REVERT: A  511 ASN cc_start: 0.8285 (t0) cc_final: 0.7909 (m-40)
REVERT: A  522 TRP cc_start: 0.7287 (t-100) cc_final: 0.5238 (t60)
REVERT: B  125 ARG cc_start: 0.6984 (pmt170) cc_final: 0.6124 (ptt180)
REVERT: B  241 TYR cc_start: 0.8001 (t80) cc_final: 0.7583 (t80)
REVERT: B  246 TYR cc_start: 0.8094 (m-10) cc_final: 0.7787 (m-80)
REVERT: B  273 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7178 (tm-30)
REVERT: B  275 VAL cc_start: 0.8169 (t) cc_final: 0.7931 (t)
REVERT: B  468 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7655 (mm)
REVERT: B  522 TRP cc_start: 0.7409 (t-100) cc_final: 0.5196 (t60)
  outliers start: 16
  outliers final: 6
  residues processed: 233
  average time/residue: 0.2117
  time to fit residues: 64.5426
Evaluate side-chains
  139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 268 HIS
B 268 HIS
B 296 GLN
B 511 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.202520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.176345 restraints weight = 7704.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.180761 restraints weight = 4352.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.183633 restraints weight = 3068.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6780  Z= 0.227
  Angle     :  0.695  13.063   9272  Z= 0.349
  Chirality :  0.041   0.163   1022
  Planarity :  0.005   0.037   1100
  Dihedral  :  6.749  50.407   1016
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 14.37 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.28), residues: 782
  helix: -0.53 (0.20), residues: 606
  sheet:  None (None), residues: 0
  loop : -3.70 (0.41), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 188 
 HIS   0.006   0.001   HIS B 425 
 PHE   0.027   0.002   PHE A 398 
 TYR   0.011   0.001   TYR B 299 
 ARG   0.003   0.001   ARG B 350 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 146
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6789 (pmt170) cc_final: 0.6443 (ptt-90)
REVERT: A  129 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7673 (mt)
REVERT: A  151 LEU cc_start: 0.8617 (tt) cc_final: 0.8123 (mt)
REVERT: A  161 TYR cc_start: 0.6965 (t80) cc_final: 0.6580 (t80)
REVERT: A  273 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6792 (tm-30)
REVERT: A  291 ILE cc_start: 0.7671 (mp) cc_final: 0.7391 (tp)
REVERT: A  297 TYR cc_start: 0.8548 (t80) cc_final: 0.7952 (t80)
REVERT: A  439 PHE cc_start: 0.4587 (m-10) cc_final: 0.4382 (m-10)
REVERT: A  522 TRP cc_start: 0.7170 (t-100) cc_final: 0.5163 (t60)
REVERT: B  125 ARG cc_start: 0.6917 (pmt170) cc_final: 0.6150 (ptt180)
REVERT: B  129 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7693 (mt)
REVERT: B  161 TYR cc_start: 0.6940 (t80) cc_final: 0.6647 (t80)
REVERT: B  297 TYR cc_start: 0.8513 (t80) cc_final: 0.7979 (t80)
REVERT: B  402 MET cc_start: 0.6150 (ptt) cc_final: 0.5773 (ptt)
REVERT: B  522 TRP cc_start: 0.7226 (t-100) cc_final: 0.5239 (t60)
  outliers start: 39
  outliers final: 26
  residues processed: 177
  average time/residue: 0.1621
  time to fit residues: 39.3143
Evaluate side-chains
  155 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0770
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   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 296 GLN
A 511 ASN
B 204 GLN
B 260 GLN
B 511 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.210911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.186186 restraints weight = 7583.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.190325 restraints weight = 4415.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.193031 restraints weight = 3122.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6780  Z= 0.190
  Angle     :  0.671  13.321   9272  Z= 0.328
  Chirality :  0.041   0.184   1022
  Planarity :  0.005   0.058   1100
  Dihedral  :  6.249  52.901   1012
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 17.13 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.30), residues: 782
  helix:  0.22 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -3.53 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 522 
 HIS   0.010   0.001   HIS A 205 
 PHE   0.022   0.001   PHE B 481 
 TYR   0.012   0.001   TYR B 404 
 ARG   0.004   0.001   ARG A 219 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 142
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6552 (pmt170) cc_final: 0.5906 (ptt180)
REVERT: A  129 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7738 (mt)
REVERT: A  161 TYR cc_start: 0.6962 (t80) cc_final: 0.6528 (t80)
REVERT: A  291 ILE cc_start: 0.7583 (mp) cc_final: 0.7320 (tp)
REVERT: A  297 TYR cc_start: 0.8545 (t80) cc_final: 0.8066 (t80)
REVERT: A  299 TYR cc_start: 0.6802 (t80) cc_final: 0.6533 (t80)
REVERT: A  478 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7245 (tm)
REVERT: A  522 TRP cc_start: 0.7153 (t-100) cc_final: 0.5275 (t60)
REVERT: B  125 ARG cc_start: 0.6507 (pmt170) cc_final: 0.5907 (ptt180)
REVERT: B  129 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7754 (mt)
REVERT: B  231 GLN cc_start: 0.7301 (pt0) cc_final: 0.7096 (pt0)
REVERT: B  297 TYR cc_start: 0.8502 (t80) cc_final: 0.8092 (t80)
REVERT: B  299 TYR cc_start: 0.6779 (t80) cc_final: 0.6487 (t80)
REVERT: B  506 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8184 (p)
REVERT: B  522 TRP cc_start: 0.7169 (t-100) cc_final: 0.5210 (t60)
  outliers start: 43
  outliers final: 27
  residues processed: 173
  average time/residue: 0.1617
  time to fit residues: 37.9214
Evaluate side-chains
  160 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  390 ASN
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  506 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.210760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.186287 restraints weight = 7646.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.190228 restraints weight = 4544.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.192518 restraints weight = 3253.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6780  Z= 0.203
  Angle     :  0.686  13.333   9272  Z= 0.330
  Chirality :  0.042   0.165   1022
  Planarity :  0.005   0.046   1100
  Dihedral  :  6.284  54.864   1012
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 19.11 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.30), residues: 782
  helix:  0.30 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.70 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 427 
 HIS   0.005   0.001   HIS A 425 
 PHE   0.020   0.001   PHE A 254 
 TYR   0.014   0.001   TYR B 430 
 ARG   0.008   0.001   ARG B 219 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.5894 (ptmt) cc_final: 0.5595 (pttp)
REVERT: A  125 ARG cc_start: 0.6492 (pmt170) cc_final: 0.5798 (ptt180)
REVERT: A  129 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7747 (mt)
REVERT: A  259 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6816 (mm-30)
REVERT: A  291 ILE cc_start: 0.7547 (mp) cc_final: 0.7292 (tp)
REVERT: A  297 TYR cc_start: 0.8571 (t80) cc_final: 0.8063 (t80)
REVERT: A  299 TYR cc_start: 0.6746 (t80) cc_final: 0.6426 (t80)
REVERT: A  478 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7274 (tm)
REVERT: A  482 PHE cc_start: 0.6677 (m-80) cc_final: 0.6455 (m-80)
REVERT: A  522 TRP cc_start: 0.7162 (t-100) cc_final: 0.5259 (t60)
REVERT: B  125 ARG cc_start: 0.6531 (pmt170) cc_final: 0.5957 (ptt180)
REVERT: B  129 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7757 (mt)
REVERT: B  297 TYR cc_start: 0.8637 (t80) cc_final: 0.8118 (t80)
REVERT: B  522 TRP cc_start: 0.7251 (t-100) cc_final: 0.5217 (t60)
  outliers start: 38
  outliers final: 28
  residues processed: 168
  average time/residue: 0.1600
  time to fit residues: 36.6725
Evaluate side-chains
  161 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.210781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.185250 restraints weight = 7635.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.189543 restraints weight = 4427.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.191897 restraints weight = 3117.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6780  Z= 0.195
  Angle     :  0.668  13.414   9272  Z= 0.321
  Chirality :  0.041   0.144   1022
  Planarity :  0.005   0.044   1100
  Dihedral  :  5.948  51.832   1012
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 19.42 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.31), residues: 782
  helix:  0.52 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.51 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 188 
 HIS   0.005   0.001   HIS A 425 
 PHE   0.023   0.001   PHE A 481 
 TYR   0.009   0.001   TYR B 472 
 ARG   0.004   0.000   ARG B 219 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 136
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.5844 (ptmt) cc_final: 0.5452 (pttp)
REVERT: A  125 ARG cc_start: 0.6453 (pmt170) cc_final: 0.5676 (ptt180)
REVERT: A  129 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7644 (mt)
REVERT: A  291 ILE cc_start: 0.7446 (mp) cc_final: 0.7245 (tp)
REVERT: A  297 TYR cc_start: 0.8505 (t80) cc_final: 0.8243 (t80)
REVERT: A  299 TYR cc_start: 0.6812 (t80) cc_final: 0.6553 (t80)
REVERT: A  468 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7620 (mp)
REVERT: A  522 TRP cc_start: 0.7377 (t-100) cc_final: 0.5281 (t60)
REVERT: B  125 ARG cc_start: 0.6554 (pmt170) cc_final: 0.5837 (ptt180)
REVERT: B  129 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7587 (mt)
REVERT: B  297 TYR cc_start: 0.8603 (t80) cc_final: 0.8399 (t80)
REVERT: B  522 TRP cc_start: 0.7349 (t-100) cc_final: 0.5194 (t60)
  outliers start: 42
  outliers final: 31
  residues processed: 172
  average time/residue: 0.1519
  time to fit residues: 36.2356
Evaluate side-chains
  168 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  390 ASN
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  506 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 32 optimal weight:    0.4980
   chunk 35 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0980
   overall best weight:    0.3958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.214524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.189877 restraints weight = 7559.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.193813 restraints weight = 4504.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.196423 restraints weight = 3238.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6780  Z= 0.166
  Angle     :  0.653  13.547   9272  Z= 0.308
  Chirality :  0.040   0.154   1022
  Planarity :  0.005   0.042   1100
  Dihedral  :  5.506  55.067   1012
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 20.34 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.32), residues: 782
  helix:  0.74 (0.22), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.30 (0.48), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 188 
 HIS   0.003   0.001   HIS A 205 
 PHE   0.023   0.001   PHE B 254 
 TYR   0.014   0.001   TYR B 210 
 ARG   0.004   0.000   ARG A 219 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.5864 (ptmt) cc_final: 0.5661 (pttp)
REVERT: A  125 ARG cc_start: 0.6384 (pmt170) cc_final: 0.5613 (ptt180)
REVERT: A  129 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7499 (mt)
REVERT: A  273 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6767 (mm-30)
REVERT: A  297 TYR cc_start: 0.8491 (t80) cc_final: 0.8074 (t80)
REVERT: A  299 TYR cc_start: 0.6730 (t80) cc_final: 0.6522 (t80)
REVERT: A  522 TRP cc_start: 0.7323 (t-100) cc_final: 0.5260 (t60)
REVERT: B  125 ARG cc_start: 0.6387 (pmt170) cc_final: 0.5699 (ptt180)
REVERT: B  129 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7477 (mt)
REVERT: B  273 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7238 (mt-10)
REVERT: B  297 TYR cc_start: 0.8563 (t80) cc_final: 0.8183 (t80)
REVERT: B  449 MET cc_start: 0.5799 (OUTLIER) cc_final: 0.3952 (tpt)
REVERT: B  522 TRP cc_start: 0.7314 (t-100) cc_final: 0.5134 (t60)
  outliers start: 31
  outliers final: 26
  residues processed: 170
  average time/residue: 0.1527
  time to fit residues: 36.4709
Evaluate side-chains
  166 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  449 MET
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  506 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0170
   chunk 32 optimal weight:    7.9990
   overall best weight:    1.2024

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
B 390 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.214425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.192094 restraints weight = 7613.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.195212 restraints weight = 4988.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.197276 restraints weight = 3812.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6780  Z= 0.255
  Angle     :  0.703  13.298   9272  Z= 0.339
  Chirality :  0.043   0.154   1022
  Planarity :  0.005   0.041   1100
  Dihedral  :  5.627  51.680   1010
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 20.03 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.31), residues: 782
  helix:  0.52 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.22 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 188 
 HIS   0.007   0.001   HIS B 425 
 PHE   0.020   0.001   PHE A 481 
 TYR   0.013   0.001   TYR A 308 
 ARG   0.003   0.000   ARG A 219 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A  265 MET cc_start: 0.8440 (mtp) cc_final: 0.8213 (mtp)
REVERT: A  297 TYR cc_start: 0.8710 (t80) cc_final: 0.8466 (t80)
REVERT: A  390 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6444 (t0)
REVERT: A  522 TRP cc_start: 0.7323 (t-100) cc_final: 0.5355 (t60)
REVERT: B  125 ARG cc_start: 0.6561 (pmt170) cc_final: 0.5960 (ptt180)
REVERT: B  129 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7752 (mt)
REVERT: B  297 TYR cc_start: 0.8693 (t80) cc_final: 0.8466 (t80)
REVERT: B  522 TRP cc_start: 0.7445 (t-100) cc_final: 0.5301 (t60)
  outliers start: 37
  outliers final: 32
  residues processed: 169
  average time/residue: 0.1479
  time to fit residues: 35.0772
Evaluate side-chains
  167 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  390 ASN
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  390 ASN
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain B residue  506 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0070
   chunk 58 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 25 optimal weight:    0.2980
   chunk 3 optimal weight:    0.6980
   chunk 34 optimal weight:    8.9990
   chunk 37 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
B 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.220216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.198346 restraints weight = 7560.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.201446 restraints weight = 4977.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.203495 restraints weight = 3769.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.4425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6780  Z= 0.179
  Angle     :  0.658  13.531   9272  Z= 0.315
  Chirality :  0.041   0.148   1022
  Planarity :  0.005   0.044   1100
  Dihedral  :  5.409  56.000   1010
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 21.10 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.31), residues: 782
  helix:  0.77 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.13 (0.49), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 188 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.019   0.001   PHE B 398 
 TYR   0.014   0.001   TYR B 210 
 ARG   0.003   0.000   ARG A 219 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.5930 (ptt-90) cc_final: 0.5323 (ptt180)
REVERT: A  265 MET cc_start: 0.8337 (mtp) cc_final: 0.8134 (mtp)
REVERT: A  273 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6691 (mm-30)
REVERT: A  297 TYR cc_start: 0.8583 (t80) cc_final: 0.8357 (t80)
REVERT: A  299 TYR cc_start: 0.6629 (t80) cc_final: 0.6313 (t80)
REVERT: A  413 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.6113 (t80)
REVERT: A  522 TRP cc_start: 0.7359 (t-100) cc_final: 0.5413 (t60)
REVERT: B  125 ARG cc_start: 0.6441 (pmt170) cc_final: 0.5832 (ptt180)
REVERT: B  129 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7561 (mt)
REVERT: B  273 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7172 (mt-10)
REVERT: B  297 TYR cc_start: 0.8564 (t80) cc_final: 0.8249 (t80)
REVERT: B  299 TYR cc_start: 0.6655 (t80) cc_final: 0.6361 (t80)
REVERT: B  522 TRP cc_start: 0.7320 (t-100) cc_final: 0.5196 (t60)
  outliers start: 31
  outliers final: 28
  residues processed: 162
  average time/residue: 0.1486
  time to fit residues: 33.7405
Evaluate side-chains
  159 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  390 ASN
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 71 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.217544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.195587 restraints weight = 7646.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.198578 restraints weight = 4974.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.200418 restraints weight = 3763.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.4476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6780  Z= 0.214
  Angle     :  0.687  13.434   9272  Z= 0.333
  Chirality :  0.043   0.148   1022
  Planarity :  0.005   0.042   1100
  Dihedral  :  5.455  54.147   1010
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 20.64 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.31), residues: 782
  helix:  0.71 (0.21), residues: 604
  sheet:  None (None), residues: 0
  loop : -3.03 (0.47), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 188 
 HIS   0.005   0.001   HIS A 425 
 PHE   0.035   0.001   PHE A 334 
 TYR   0.013   0.001   TYR A 210 
 ARG   0.003   0.000   ARG A 219 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.5977 (ptt-90) cc_final: 0.5381 (ptt180)
REVERT: A  212 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7561 (mttt)
REVERT: A  297 TYR cc_start: 0.8656 (t80) cc_final: 0.8414 (t80)
REVERT: A  413 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.6190 (t80)
REVERT: A  522 TRP cc_start: 0.7409 (t-100) cc_final: 0.5405 (t60)
REVERT: B  297 TYR cc_start: 0.8632 (t80) cc_final: 0.8406 (t80)
REVERT: B  522 TRP cc_start: 0.7353 (t-100) cc_final: 0.5141 (t60)
  outliers start: 34
  outliers final: 31
  residues processed: 161
  average time/residue: 0.1556
  time to fit residues: 35.3606
Evaluate side-chains
  163 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0040
   chunk 49 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0770
   chunk 32 optimal weight:    8.9990
   chunk 67 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.4750

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

Flipped N/Q/H residues before XYZ refinement:
A 386 HIS
B 390 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.221470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.199501 restraints weight = 7671.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.202597 restraints weight = 4988.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.204702 restraints weight = 3779.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.4728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6780  Z= 0.178
  Angle     :  0.658  13.755   9272  Z= 0.316
  Chirality :  0.041   0.145   1022
  Planarity :  0.005   0.041   1100
  Dihedral  :  5.299  57.982   1010
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.64 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.31), residues: 782
  helix:  0.81 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.95 (0.49), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 188 
 HIS   0.003   0.001   HIS A 215 
 PHE   0.034   0.001   PHE A 334 
 TYR   0.015   0.001   TYR A 210 
 ARG   0.003   0.000   ARG B 350 

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 138
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.5970 (ptt-90) cc_final: 0.5365 (ptt180)
REVERT: A  129 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7569 (mt)
REVERT: A  212 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7566 (mttt)
REVERT: A  273 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6756 (mm-30)
REVERT: A  297 TYR cc_start: 0.8560 (t80) cc_final: 0.8314 (t80)
REVERT: A  413 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.6173 (t80)
REVERT: A  449 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.4067 (tpt)
REVERT: A  522 TRP cc_start: 0.7359 (t-100) cc_final: 0.5336 (t60)
REVERT: B  125 ARG cc_start: 0.5786 (ptt-90) cc_final: 0.5182 (ptt180)
REVERT: B  273 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7165 (mt-10)
REVERT: B  297 TYR cc_start: 0.8572 (t80) cc_final: 0.8234 (t80)
REVERT: B  299 TYR cc_start: 0.6758 (t80) cc_final: 0.6415 (t80)
  outliers start: 35
  outliers final: 29
  residues processed: 165
  average time/residue: 0.1428
  time to fit residues: 33.2743
Evaluate side-chains
  164 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  269 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  390 ASN
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 72 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.220373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.198310 restraints weight = 7784.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.201382 restraints weight = 4997.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.203354 restraints weight = 3764.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6780  Z= 0.235
  Angle     :  1.028  59.200   9272  Z= 0.584
  Chirality :  0.051   0.959   1022
  Planarity :  0.006   0.092   1100
  Dihedral  :  5.359  58.001   1010
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 21.56 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.31), residues: 782
  helix:  0.81 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.93 (0.49), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 188 
 HIS   0.003   0.001   HIS B 425 
 PHE   0.028   0.001   PHE A 334 
 TYR   0.014   0.001   TYR A 210 
 ARG   0.002   0.000   ARG B 350 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2047.27 seconds
wall clock time: 37 minutes 27.99 seconds (2247.99 seconds total)