Starting phenix.real_space_refine
on Tue Mar 11 20:08:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6l48_0832/03_2025/6l48_0832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l48_0832/03_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_0832/03_2025/6l48_0832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l48_0832/03_2025/6l48_0832.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l48_0832/03_2025/6l48_0832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l48_0832/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.66, per 1000 atoms: 0.87
  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: 1.73
  Conformation dependent library (CDL) restraints added in 840.8 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: 0.67
  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: 1.67

  Time building geometry restraints manager: 2.06 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:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.950
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.730
-------------------------------------------------------------------------------
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  : 0.670 
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: 0.1949
  time to fit residues: 59.1411
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  : 0.681 
-------------------------------------------------------------------------------
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 = 43)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.180662 restraints weight = 4352.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.183602 restraints weight = 3086.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
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  : 0.765 
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: 0.8618 (tt) cc_final: 0.8124 (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: 0.8549 (t80) cc_final: 0.7953 (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: 0.8006 (OUTLIER) cc_final: 0.7694 (mt)
REVERT: B  161 TYR cc_start: 0.6939 (t80) cc_final: 0.6647 (t80)
REVERT: B  297 TYR cc_start: 0.8513 (t80) cc_final: 0.7980 (t80)
REVERT: B  402 MET cc_start: 0.6151 (ptt) cc_final: 0.5774 (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: 0.1684
  time to fit residues: 41.1843
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  : 0.708 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0570
   chunk 2 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.4444 r_free = 0.4444 target = 0.210964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.186212 restraints weight = 7574.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.190361 restraints weight = 4427.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.193014 restraints weight = 3130.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.3099

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= 0.194
  Angle     :  0.675  13.336   9272  Z= 0.329
  Chirality :  0.041   0.186   1022
  Planarity :  0.005   0.060   1100
  Dihedral  :  6.251  52.628   1012
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 17.43 %
    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: -1.08 (0.30), residues: 782
  helix:  0.21 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -3.54 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 188 
 HIS   0.009   0.001   HIS A 205 
 PHE   0.021   0.001   PHE B 481 
 TYR   0.012   0.001   TYR B 404 
 ARG   0.005   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
  183 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6556 (pmt170) cc_final: 0.5906 (ptt180)
REVERT: A  129 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7746 (mt)
REVERT: A  161 TYR cc_start: 0.6964 (t80) cc_final: 0.6529 (t80)
REVERT: A  291 ILE cc_start: 0.7602 (mp) cc_final: 0.7297 (tp)
REVERT: A  297 TYR cc_start: 0.8552 (t80) cc_final: 0.8069 (t80)
REVERT: A  478 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7243 (tm)
REVERT: A  482 PHE cc_start: 0.6407 (m-80) cc_final: 0.6156 (m-80)
REVERT: A  522 TRP cc_start: 0.7241 (t-100) cc_final: 0.5392 (t60)
REVERT: B  125 ARG cc_start: 0.6515 (pmt170) cc_final: 0.5915 (ptt180)
REVERT: B  129 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7742 (mt)
REVERT: B  231 GLN cc_start: 0.7311 (pt0) cc_final: 0.7066 (pt0)
REVERT: B  297 TYR cc_start: 0.8507 (t80) cc_final: 0.8092 (t80)
REVERT: B  299 TYR cc_start: 0.6725 (t80) cc_final: 0.6415 (t80)
REVERT: B  506 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8182 (p)
REVERT: B  522 TRP cc_start: 0.7175 (t-100) cc_final: 0.5221 (t60)
  outliers start: 41
  outliers final: 27
  residues processed: 173
  average time/residue: 0.1676
  time to fit residues: 39.5374
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  : 0.736 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 55 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.211410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.185792 restraints weight = 7670.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.190039 restraints weight = 4466.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.192819 restraints weight = 3161.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6780  Z= 0.191
  Angle     :  0.677  13.362   9272  Z= 0.325
  Chirality :  0.041   0.162   1022
  Planarity :  0.005   0.046   1100
  Dihedral  :  6.219  53.100   1012
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 19.11 %
    Favored  : 75.23 %
  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: -0.81 (0.31), residues: 782
  helix:  0.36 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.67 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 427 
 HIS   0.005   0.001   HIS B 425 
 PHE   0.020   0.001   PHE B 254 
 TYR   0.014   0.001   TYR B 430 
 ARG   0.004   0.001   ARG A 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
  172 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 135
  time to evaluate  : 0.676 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6448 (pmt170) cc_final: 0.5667 (ptt180)
REVERT: A  129 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7658 (mt)
REVERT: A  259 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6914 (mm-30)
REVERT: A  291 ILE cc_start: 0.7549 (mp) cc_final: 0.7255 (tp)
REVERT: A  297 TYR cc_start: 0.8529 (t80) cc_final: 0.8022 (t80)
REVERT: A  478 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7288 (tm)
REVERT: A  522 TRP cc_start: 0.7177 (t-100) cc_final: 0.5214 (t60)
REVERT: B  125 ARG cc_start: 0.6531 (pmt170) cc_final: 0.5887 (ptt180)
REVERT: B  129 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7680 (mt)
REVERT: B  297 TYR cc_start: 0.8598 (t80) cc_final: 0.8080 (t80)
REVERT: B  522 TRP cc_start: 0.7248 (t-100) cc_final: 0.5157 (t60)
  outliers start: 37
  outliers final: 27
  residues processed: 167
  average time/residue: 0.1689
  time to fit residues: 39.0136
Evaluate side-chains
  159 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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  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:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 21 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0970
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.4463 r_free = 0.4463 target = 0.213357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.187855 restraints weight = 7630.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.191977 restraints weight = 4418.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.194754 restraints weight = 3145.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.3832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6780  Z= 0.179
  Angle     :  0.663  13.482   9272  Z= 0.317
  Chirality :  0.041   0.219   1022
  Planarity :  0.005   0.042   1100
  Dihedral  :  6.060  54.422   1012
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 19.57 %
    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: -0.50 (0.31), residues: 782
  helix:  0.57 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.57 (0.47), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 425 
 PHE   0.024   0.001   PHE A 481 
 TYR   0.013   0.001   TYR B 210 
 ARG   0.005   0.000   ARG A 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: 40
    poor density    : 138
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5341 (pttp)
REVERT: A  125 ARG cc_start: 0.6421 (pmt170) cc_final: 0.5594 (ptt180)
REVERT: A  129 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7564 (mt)
REVERT: A  291 ILE cc_start: 0.7368 (mp) cc_final: 0.7163 (tp)
REVERT: A  297 TYR cc_start: 0.8471 (t80) cc_final: 0.8008 (t80)
REVERT: A  468 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7615 (mp)
REVERT: A  478 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7266 (tm)
REVERT: A  522 TRP cc_start: 0.7220 (t-100) cc_final: 0.5208 (t60)
REVERT: B  125 ARG cc_start: 0.6480 (pmt170) cc_final: 0.5776 (ptt180)
REVERT: B  129 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7547 (mt)
REVERT: B  297 TYR cc_start: 0.8573 (t80) cc_final: 0.8356 (t80)
REVERT: B  522 TRP cc_start: 0.7325 (t-100) cc_final: 0.5200 (t60)
  outliers start: 40
  outliers final: 33
  residues processed: 170
  average time/residue: 0.1437
  time to fit residues: 34.2017
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  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LYS
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  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 A residue  478 LEU
Chi-restraints excluded: chain A residue  506 SER
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  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:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 50 optimal weight:    0.2980
   chunk 32 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0670
   chunk 66 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.4477 r_free = 0.4477 target = 0.214911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.190151 restraints weight = 7564.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.194103 restraints weight = 4528.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.196712 restraints weight = 3266.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.4304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.4111

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= 0.169
  Angle     :  0.648  13.498   9272  Z= 0.308
  Chirality :  0.041   0.211   1022
  Planarity :  0.005   0.040   1100
  Dihedral  :  5.568  56.917   1012
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 20.03 %
    Favored  : 74.46 %
  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:  0.80 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -3.40 (0.47), residues: 178

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   0.022   0.001   PHE A 254 
 TYR   0.016   0.001   TYR A 210 
 ARG   0.006   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
  178 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.5614 (ptmt) cc_final: 0.5204 (pttp)
REVERT: A  125 ARG cc_start: 0.6324 (pmt170) cc_final: 0.5551 (ptt180)
REVERT: A  129 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7515 (mt)
REVERT: A  273 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6776 (mm-30)
REVERT: A  297 TYR cc_start: 0.8490 (t80) cc_final: 0.8111 (t80)
REVERT: A  478 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7299 (tm)
REVERT: A  522 TRP cc_start: 0.7331 (t-100) cc_final: 0.5242 (t60)
REVERT: B  125 ARG cc_start: 0.6442 (pmt170) cc_final: 0.5704 (ptt180)
REVERT: B  129 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7532 (mt)
REVERT: B  191 MET cc_start: 0.7598 (ttm) cc_final: 0.7391 (ttm)
REVERT: B  297 TYR cc_start: 0.8613 (t80) cc_final: 0.8309 (t80)
REVERT: B  522 TRP cc_start: 0.7315 (t-100) cc_final: 0.5139 (t60)
  outliers start: 36
  outliers final: 28
  residues processed: 170
  average time/residue: 0.1439
  time to fit residues: 34.7894
Evaluate side-chains
  167 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 135
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
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  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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS
A 215 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.216021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.193831 restraints weight = 7591.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.196856 restraints weight = 4959.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.198887 restraints weight = 3764.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6780  Z= 0.236
  Angle     :  0.692  13.359   9272  Z= 0.335
  Chirality :  0.043   0.192   1022
  Planarity :  0.005   0.041   1100
  Dihedral  :  5.634  55.004   1011
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 20.03 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.41 (0.31), residues: 782
  helix:  0.56 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.22 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 188 
 HIS   0.009   0.001   HIS A 205 
 PHE   0.021   0.001   PHE A 481 
 TYR   0.013   0.001   TYR A 308 
 ARG   0.004   0.001   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
  170 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.5547 (ptmt) cc_final: 0.5088 (pttp)
REVERT: A  191 MET cc_start: 0.7617 (ttm) cc_final: 0.7388 (ttm)
REVERT: A  265 MET cc_start: 0.8486 (mtp) cc_final: 0.8241 (mtp)
REVERT: A  297 TYR cc_start: 0.8676 (t80) cc_final: 0.8368 (t80)
REVERT: A  390 ASN cc_start: 0.6662 (OUTLIER) cc_final: 0.6450 (t0)
REVERT: A  478 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7547 (tm)
REVERT: A  522 TRP cc_start: 0.7346 (t-100) cc_final: 0.5356 (t60)
REVERT: B  125 ARG cc_start: 0.6591 (pmt170) cc_final: 0.5970 (ptt180)
REVERT: B  129 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7644 (mt)
REVERT: B  297 TYR cc_start: 0.8725 (t80) cc_final: 0.8497 (t80)
REVERT: B  522 TRP cc_start: 0.7497 (t-100) cc_final: 0.5373 (t60)
  outliers start: 40
  outliers final: 34
  residues processed: 162
  average time/residue: 0.1431
  time to fit residues: 32.9574
Evaluate side-chains
  167 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 130
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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  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  474 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  506 SER
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0980
   chunk 58 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 34 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.219563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.197502 restraints weight = 7584.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.200676 restraints weight = 4954.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.202739 restraints weight = 3752.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.4366

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= 0.189
  Angle     :  0.656  13.508   9272  Z= 0.317
  Chirality :  0.041   0.185   1022
  Planarity :  0.005   0.041   1100
  Dihedral  :  5.415  57.049   1011
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 20.34 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.31), residues: 782
  helix:  0.78 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.11 (0.48), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 188 
 HIS   0.008   0.001   HIS A 205 
 PHE   0.022   0.001   PHE B 254 
 TYR   0.013   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
  171 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 132
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.5329 (ptmt) cc_final: 0.4990 (pttp)
REVERT: A  125 ARG cc_start: 0.5936 (ptt-90) cc_final: 0.5265 (ptt180)
REVERT: A  297 TYR cc_start: 0.8545 (t80) cc_final: 0.8204 (t80)
REVERT: A  478 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7518 (tm)
REVERT: A  482 PHE cc_start: 0.6688 (m-80) cc_final: 0.6357 (m-80)
REVERT: A  522 TRP cc_start: 0.7342 (t-100) cc_final: 0.5364 (t60)
REVERT: B  125 ARG cc_start: 0.6461 (pmt170) cc_final: 0.5849 (ptt180)
REVERT: B  129 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7601 (mt)
REVERT: B  297 TYR cc_start: 0.8607 (t80) cc_final: 0.8341 (t80)
REVERT: B  522 TRP cc_start: 0.7315 (t-100) cc_final: 0.5204 (t60)
  outliers start: 39
  outliers final: 31
  residues processed: 164
  average time/residue: 0.1362
  time to fit residues: 31.8441
Evaluate side-chains
  162 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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  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  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 A residue  506 SER
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  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  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:    0.0070
   chunk 75 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS
A 386 HIS
B 386 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.219680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.197486 restraints weight = 7637.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.200622 restraints weight = 4963.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.202686 restraints weight = 3742.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.4563

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= 0.186
  Angle     :  0.648  13.511   9272  Z= 0.311
  Chirality :  0.041   0.173   1022
  Planarity :  0.005   0.041   1100
  Dihedral  :  5.280  57.141   1010
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 20.64 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.05 (0.31), residues: 782
  helix:  0.80 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.94 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 388 
 HIS   0.009   0.001   HIS A 205 
 PHE   0.020   0.001   PHE B 481 
 TYR   0.013   0.001   TYR B 210 
 ARG   0.003   0.000   ARG B 272 

*********************** 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
  173 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.5947 (ptt-90) cc_final: 0.5314 (ptt180)
REVERT: A  212 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7546 (mttt)
REVERT: A  297 TYR cc_start: 0.8572 (t80) cc_final: 0.8215 (t80)
REVERT: A  413 TYR cc_start: 0.6542 (OUTLIER) cc_final: 0.6183 (t80)
REVERT: A  478 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7586 (tm)
REVERT: A  482 PHE cc_start: 0.6704 (m-80) cc_final: 0.6474 (m-80)
REVERT: A  522 TRP cc_start: 0.7365 (t-100) cc_final: 0.5350 (t60)
REVERT: B  129 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7556 (mt)
REVERT: B  297 TYR cc_start: 0.8586 (t80) cc_final: 0.8307 (t80)
REVERT: B  299 TYR cc_start: 0.6733 (t80) cc_final: 0.6465 (t80)
REVERT: B  522 TRP cc_start: 0.7400 (t-100) cc_final: 0.5275 (t60)
  outliers start: 36
  outliers final: 30
  residues processed: 167
  average time/residue: 0.1419
  time to fit residues: 33.7630
Evaluate side-chains
  159 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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  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 A residue  478 LEU
Chi-restraints excluded: chain A residue  506 SER
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  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  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:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 73 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS
A 390 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.219520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.198158 restraints weight = 7627.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.201171 restraints weight = 4922.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.203008 restraints weight = 3711.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.4670

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= 0.200
  Angle     :  0.657  13.586   9272  Z= 0.321
  Chirality :  0.042   0.180   1022
  Planarity :  0.005   0.041   1100
  Dihedral  :  5.241  55.827   1010
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  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: -0.02 (0.31), residues: 782
  helix:  0.82 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.91 (0.49), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 188 
 HIS   0.009   0.001   HIS A 205 
 PHE   0.024   0.001   PHE A 481 
 TYR   0.014   0.001   TYR B 210 
 ARG   0.003   0.000   ARG B 272 

********************** 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
  165 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 130
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.5980 (ptt-90) cc_final: 0.5414 (ptt180)
REVERT: A  212 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7530 (mttt)
REVERT: A  273 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6387 (mt-10)
REVERT: A  297 TYR cc_start: 0.8572 (t80) cc_final: 0.8148 (t80)
REVERT: A  413 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.6186 (t80)
REVERT: A  478 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7533 (tm)
REVERT: A  482 PHE cc_start: 0.6673 (m-80) cc_final: 0.6391 (m-80)
REVERT: A  522 TRP cc_start: 0.7369 (t-100) cc_final: 0.5344 (t60)
REVERT: B  125 ARG cc_start: 0.5990 (ptt-90) cc_final: 0.5387 (ptt180)
REVERT: B  129 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7664 (mt)
REVERT: B  297 TYR cc_start: 0.8626 (t80) cc_final: 0.8372 (t80)
  outliers start: 35
  outliers final: 29
  residues processed: 161
  average time/residue: 0.1402
  time to fit residues: 32.1132
Evaluate side-chains
  157 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  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  217 LEU
Chi-restraints excluded: chain A residue  220 SER
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  390 ASN
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 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  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  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:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0170
   chunk 31 optimal weight:    4.9990
   chunk 66 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS
A 390 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.220462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.198276 restraints weight = 7760.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.201401 restraints weight = 4983.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.203528 restraints weight = 3749.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.4752

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= 0.182
  Angle     :  0.651  13.764   9272  Z= 0.314
  Chirality :  0.042   0.177   1022
  Planarity :  0.005   0.042   1100
  Dihedral  :  5.172  56.705   1010
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 20.95 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.04 (0.31), residues: 782
  helix:  0.84 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.86 (0.50), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 188 
 HIS   0.009   0.001   HIS A 205 
 PHE   0.025   0.001   PHE A 481 
 TYR   0.014   0.001   TYR B 210 
 ARG   0.003   0.000   ARG B 272 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2136.02 seconds
wall clock time: 37 minutes 52.08 seconds (2272.08 seconds total)