Starting phenix.real_space_refine
on Tue Mar  3 15:27:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6l48_0832/03_2026/6l48_0832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l48_0832/03_2026/6l48_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l48_0832/03_2026/6l48_0832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l48_0832/03_2026/6l48_0832.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6l48_0832/03_2026/6l48_0832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l48_0832/03_2026/6l48_0832.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'PHE:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          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: 1.96, per 1000 atoms: 0.30
  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: 0.65
  Conformation dependent library (CDL) restraints added in 240.4 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: 0.11
  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: 0.84

  Time building geometry restraints manager: 0.83 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.750
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.870
-------------------------------------------------------------------------------
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= 0.174
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG B 350 
 TYR   0.013   0.001   TYR B 433 
 PHE   0.015   0.001   PHE A 331 
 TRP   0.011   0.001   TRP B 504 
 HIS   0.008   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6780)
  covalent geometry    : angle       0.76160 ( 9272)
  hydrogen bonds       : bond        0.09525 (  472)
  hydrogen bonds       : angle       7.79531 ( 1416)

*********************** 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  : 0.226 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.7028 (pmt170) cc_final: 0.6719 (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: 0.5239 (t60)
REVERT: B  125 ARG cc_start: 0.6984 (pmt170) cc_final: 0.6125 (ptt180)
REVERT: B  241 TYR cc_start: 0.8001 (t80) cc_final: 0.7584 (t80)
REVERT: B  246 TYR cc_start: 0.8094 (m-10) cc_final: 0.7786 (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: 0.0789
  time to fit residues: 24.0335
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  : 0.199 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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 = 0.4386 r_free = 0.4386 target = 0.204199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.177944 restraints weight = 7687.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.182475 restraints weight = 4296.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.185500 restraints weight = 2985.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.187196 restraints weight = 2347.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.188699 restraints weight = 2018.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6780  Z= 0.163
  Angle     :  0.691  12.919   9272  Z= 0.348
  Chirality :  0.042   0.164   1022
  Planarity :  0.005   0.038   1100
  Dihedral  :  6.790  48.695   1016
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 14.98 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.29), residues: 782
  helix: -0.39 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -3.78 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 219 
 TYR   0.012   0.001   TYR A 336 
 PHE   0.017   0.002   PHE B 254 
 TRP   0.012   0.001   TRP A 188 
 HIS   0.006   0.001   HIS B 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6780)
  covalent geometry    : angle       0.69091 ( 9272)
  hydrogen bonds       : bond        0.04190 (  472)
  hydrogen bonds       : angle       6.16240 ( 1416)

*********************** 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
  183 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6880 (pmt170) cc_final: 0.6529 (ptt-90)
REVERT: A  129 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7532 (mt)
REVERT: A  151 LEU cc_start: 0.8528 (tt) cc_final: 0.8051 (mt)
REVERT: A  161 TYR cc_start: 0.6970 (t80) cc_final: 0.6592 (t80)
REVERT: A  273 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6807 (tm-30)
REVERT: A  291 ILE cc_start: 0.7705 (mp) cc_final: 0.7380 (tp)
REVERT: A  297 TYR cc_start: 0.8498 (t80) cc_final: 0.7859 (t80)
REVERT: A  439 PHE cc_start: 0.4568 (m-10) cc_final: 0.4352 (m-10)
REVERT: A  522 TRP cc_start: 0.7129 (t-100) cc_final: 0.5207 (t60)
REVERT: B  125 ARG cc_start: 0.6849 (pmt170) cc_final: 0.6124 (ptt180)
REVERT: B  129 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7529 (mt)
REVERT: B  161 TYR cc_start: 0.6944 (t80) cc_final: 0.6654 (t80)
REVERT: B  291 ILE cc_start: 0.7962 (mp) cc_final: 0.7758 (tp)
REVERT: B  297 TYR cc_start: 0.8448 (t80) cc_final: 0.7890 (t80)
REVERT: B  439 PHE cc_start: 0.4689 (m-10) cc_final: 0.4433 (m-10)
REVERT: B  522 TRP cc_start: 0.7321 (t-100) cc_final: 0.5378 (t60)
  outliers start: 38
  outliers final: 24
  residues processed: 176
  average time/residue: 0.0655
  time to fit residues: 16.1052
Evaluate side-chains
  150 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
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  330 VAL
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  474 VAL
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  129 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  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 23 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:    0.4980
   chunk 4 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 511 ASN
B 204 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 = 0.4425 r_free = 0.4425 target = 0.208753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.184535 restraints weight = 7546.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.188405 restraints weight = 4462.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.190958 restraints weight = 3209.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.192635 restraints weight = 2569.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.193577 restraints weight = 2214.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3143

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= 0.147
  Angle     :  0.674  12.667   9272  Z= 0.331
  Chirality :  0.042   0.182   1022
  Planarity :  0.005   0.062   1100
  Dihedral  :  6.322  51.271   1012
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 16.97 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.30), residues: 782
  helix:  0.15 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -3.56 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 350 
 TYR   0.010   0.001   TYR B 404 
 PHE   0.020   0.001   PHE B 481 
 TRP   0.013   0.001   TRP B 427 
 HIS   0.005   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6780)
  covalent geometry    : angle       0.67416 ( 9272)
  hydrogen bonds       : bond        0.04009 (  472)
  hydrogen bonds       : angle       5.94498 ( 1416)

*********************** 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: 43
    poor density    : 140
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6566 (pmt170) cc_final: 0.5968 (ptt180)
REVERT: A  129 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7764 (mt)
REVERT: A  161 TYR cc_start: 0.6873 (t80) cc_final: 0.6453 (t80)
REVERT: A  291 ILE cc_start: 0.7573 (mp) cc_final: 0.7354 (tp)
REVERT: A  297 TYR cc_start: 0.8547 (t80) cc_final: 0.8072 (t80)
REVERT: A  299 TYR cc_start: 0.6917 (t80) cc_final: 0.6627 (t80)
REVERT: A  478 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7362 (tm)
REVERT: A  482 PHE cc_start: 0.6522 (m-80) cc_final: 0.6221 (m-80)
REVERT: A  522 TRP cc_start: 0.7155 (t-100) cc_final: 0.5345 (t60)
REVERT: B  125 ARG cc_start: 0.6784 (pmt170) cc_final: 0.6220 (ptt180)
REVERT: B  129 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7765 (mt)
REVERT: B  297 TYR cc_start: 0.8602 (t80) cc_final: 0.8154 (t80)
REVERT: B  299 TYR cc_start: 0.6737 (t80) cc_final: 0.6440 (t80)
REVERT: B  522 TRP cc_start: 0.7235 (t-100) cc_final: 0.5357 (t60)
  outliers start: 43
  outliers final: 30
  residues processed: 171
  average time/residue: 0.0669
  time to fit residues: 15.7092
Evaluate side-chains
  163 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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  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 A residue  506 SER
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  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
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 35 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4400 r_free = 0.4400 target = 0.206172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.181698 restraints weight = 7643.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.185625 restraints weight = 4544.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.188253 restraints weight = 3260.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.189682 restraints weight = 2601.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.191031 restraints weight = 2263.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.3546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6780  Z= 0.170
  Angle     :  0.709  12.437   9272  Z= 0.346
  Chirality :  0.043   0.160   1022
  Planarity :  0.005   0.049   1100
  Dihedral  :  6.301  49.488   1012
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 18.20 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.30), residues: 782
  helix:  0.17 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -3.72 (0.43), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 219 
 TYR   0.015   0.002   TYR A 308 
 PHE   0.020   0.002   PHE A 254 
 TRP   0.014   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6780)
  covalent geometry    : angle       0.70891 ( 9272)
  hydrogen bonds       : bond        0.04068 (  472)
  hydrogen bonds       : angle       5.85846 ( 1416)

*********************** 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
  182 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 138
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6539 (pmt170) cc_final: 0.5850 (ptt180)
REVERT: A  129 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7643 (mt)
REVERT: A  291 ILE cc_start: 0.7591 (mp) cc_final: 0.7367 (tp)
REVERT: A  297 TYR cc_start: 0.8661 (t80) cc_final: 0.8317 (t80)
REVERT: A  299 TYR cc_start: 0.6847 (t80) cc_final: 0.6613 (t80)
REVERT: A  478 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7505 (tm)
REVERT: A  522 TRP cc_start: 0.7286 (t-100) cc_final: 0.5335 (t60)
REVERT: B  125 ARG cc_start: 0.6599 (pmt170) cc_final: 0.5999 (ptt180)
REVERT: B  129 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7715 (mt)
REVERT: B  297 TYR cc_start: 0.8668 (t80) cc_final: 0.8364 (t80)
REVERT: B  522 TRP cc_start: 0.7337 (t-100) cc_final: 0.5381 (t60)
  outliers start: 44
  outliers final: 31
  residues processed: 174
  average time/residue: 0.0645
  time to fit residues: 15.5250
Evaluate side-chains
  165 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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  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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0470
   chunk 35 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    1.2084

-------------------------------------------------------------------------------
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 = 0.4382 r_free = 0.4382 target = 0.204743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.180358 restraints weight = 7671.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.184385 restraints weight = 4505.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.186996 restraints weight = 3198.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.188621 restraints weight = 2547.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.189742 restraints weight = 2196.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6780  Z= 0.175
  Angle     :  0.706  12.633   9272  Z= 0.345
  Chirality :  0.043   0.162   1022
  Planarity :  0.005   0.046   1100
  Dihedral  :  6.016  46.601   1012
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 19.88 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.30), residues: 782
  helix:  0.22 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.72 (0.44), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 219 
 TYR   0.013   0.001   TYR A 308 
 PHE   0.021   0.002   PHE B 481 
 TRP   0.009   0.001   TRP A 188 
 HIS   0.006   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6780)
  covalent geometry    : angle       0.70552 ( 9272)
  hydrogen bonds       : bond        0.04082 (  472)
  hydrogen bonds       : angle       5.85065 ( 1416)

*********************** 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
  183 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 139
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6553 (pmt170) cc_final: 0.5877 (ptt180)
REVERT: A  129 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7594 (mt)
REVERT: A  161 TYR cc_start: 0.6924 (t80) cc_final: 0.6507 (t80)
REVERT: A  273 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6584 (mt-10)
REVERT: A  291 ILE cc_start: 0.7592 (mp) cc_final: 0.7389 (tp)
REVERT: A  297 TYR cc_start: 0.8611 (t80) cc_final: 0.8359 (t80)
REVERT: A  299 TYR cc_start: 0.6780 (t80) cc_final: 0.6483 (t80)
REVERT: A  478 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7401 (tm)
REVERT: A  522 TRP cc_start: 0.7383 (t-100) cc_final: 0.5415 (t60)
REVERT: B  125 ARG cc_start: 0.6657 (pmt170) cc_final: 0.6019 (ptt180)
REVERT: B  129 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7633 (mt)
REVERT: B  468 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7794 (mp)
REVERT: B  522 TRP cc_start: 0.7461 (t-100) cc_final: 0.5391 (t60)
  outliers start: 44
  outliers final: 32
  residues processed: 173
  average time/residue: 0.0599
  time to fit residues: 14.8056
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  : 0.252 
-------------------------------------------------------------------------------
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  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 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  223 HIS
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  411 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 16 optimal weight:   10.0000
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.4396 r_free = 0.4396 target = 0.206125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.181675 restraints weight = 7666.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.185639 restraints weight = 4497.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.188231 restraints weight = 3203.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.190017 restraints weight = 2562.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.190965 restraints weight = 2183.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6780  Z= 0.158
  Angle     :  0.688  12.461   9272  Z= 0.333
  Chirality :  0.043   0.232   1022
  Planarity :  0.005   0.041   1100
  Dihedral  :  5.764  47.238   1012
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 19.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.31), residues: 782
  helix:  0.40 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.53 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 219 
 TYR   0.017   0.001   TYR B 297 
 PHE   0.020   0.001   PHE A 398 
 TRP   0.009   0.001   TRP A 188 
 HIS   0.007   0.001   HIS B 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6780)
  covalent geometry    : angle       0.68769 ( 9272)
  hydrogen bonds       : bond        0.03947 (  472)
  hydrogen bonds       : angle       5.75916 ( 1416)

*********************** 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
  176 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6562 (pmt170) cc_final: 0.5856 (ptt180)
REVERT: A  129 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7557 (mt)
REVERT: A  273 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6599 (mt-10)
REVERT: A  297 TYR cc_start: 0.8551 (t80) cc_final: 0.8288 (t80)
REVERT: A  299 TYR cc_start: 0.6661 (t80) cc_final: 0.6435 (t80)
REVERT: A  413 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.6061 (t80)
REVERT: A  478 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7422 (tm)
REVERT: A  522 TRP cc_start: 0.7380 (t-100) cc_final: 0.5424 (t60)
REVERT: B  125 ARG cc_start: 0.6614 (pmt170) cc_final: 0.5954 (ptt180)
REVERT: B  129 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7583 (mt)
REVERT: B  299 TYR cc_start: 0.6806 (t80) cc_final: 0.6581 (t80)
REVERT: B  411 THR cc_start: 0.6560 (OUTLIER) cc_final: 0.6341 (m)
REVERT: B  413 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.6123 (t80)
REVERT: B  468 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7699 (mp)
REVERT: B  522 TRP cc_start: 0.7381 (t-100) cc_final: 0.5265 (t60)
  outliers start: 42
  outliers final: 30
  residues processed: 169
  average time/residue: 0.0614
  time to fit residues: 14.6103
Evaluate side-chains
  166 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 128
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
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  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  275 VAL
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  411 THR
Chi-restraints excluded: chain B residue  413 TYR
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  468 LEU
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 68 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.206258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.181926 restraints weight = 7578.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.185885 restraints weight = 4451.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.188459 restraints weight = 3164.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.190098 restraints weight = 2529.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.190380 restraints weight = 2178.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.4273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6780  Z= 0.155
  Angle     :  0.685  12.908   9272  Z= 0.332
  Chirality :  0.042   0.194   1022
  Planarity :  0.005   0.043   1100
  Dihedral  :  5.640  47.339   1010
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 20.49 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.31), residues: 782
  helix:  0.44 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.31 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 219 
 TYR   0.021   0.001   TYR A 210 
 PHE   0.021   0.001   PHE A 398 
 TRP   0.008   0.001   TRP A 188 
 HIS   0.007   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6780)
  covalent geometry    : angle       0.68473 ( 9272)
  hydrogen bonds       : bond        0.03893 (  472)
  hydrogen bonds       : angle       5.69824 ( 1416)

*********************** 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
  171 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 130
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6630 (pmt170) cc_final: 0.5866 (ptt180)
REVERT: A  273 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6642 (mt-10)
REVERT: A  297 TYR cc_start: 0.8560 (t80) cc_final: 0.8353 (t80)
REVERT: A  299 TYR cc_start: 0.6756 (t80) cc_final: 0.6528 (t80)
REVERT: A  413 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.6115 (t80)
REVERT: A  449 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.4111 (tpt)
REVERT: A  478 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7098 (tm)
REVERT: A  482 PHE cc_start: 0.6753 (m-10) cc_final: 0.6532 (m-80)
REVERT: A  503 MET cc_start: 0.8004 (tmm) cc_final: 0.7668 (tmm)
REVERT: A  522 TRP cc_start: 0.7461 (t-100) cc_final: 0.5422 (t60)
REVERT: B  125 ARG cc_start: 0.6679 (pmt170) cc_final: 0.5972 (ptt180)
REVERT: B  129 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7436 (mt)
REVERT: B  151 LEU cc_start: 0.8663 (tt) cc_final: 0.8141 (mt)
REVERT: B  522 TRP cc_start: 0.7543 (t-100) cc_final: 0.5290 (t60)
  outliers start: 41
  outliers final: 34
  residues processed: 164
  average time/residue: 0.0634
  time to fit residues: 14.6334
Evaluate side-chains
  161 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 122
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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  390 ASN
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  449 MET
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain 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  187 THR
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  390 ASN
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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
B 390 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.213757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.192036 restraints weight = 7682.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.195178 restraints weight = 4942.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.197234 restraints weight = 3710.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.198350 restraints weight = 3061.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.199446 restraints weight = 2720.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.4452

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= 0.157
  Angle     :  0.696  12.584   9272  Z= 0.338
  Chirality :  0.042   0.187   1022
  Planarity :  0.005   0.040   1100
  Dihedral  :  5.605  47.081   1010
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 20.64 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.31), residues: 782
  helix:  0.49 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.34 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 219 
 TYR   0.018   0.001   TYR A 210 
 PHE   0.021   0.001   PHE A 398 
 TRP   0.009   0.001   TRP B 388 
 HIS   0.009   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6780)
  covalent geometry    : angle       0.69581 ( 9272)
  hydrogen bonds       : bond        0.03933 (  472)
  hydrogen bonds       : angle       5.71391 ( 1416)

*********************** 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
  175 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 130
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6449 (mt-10)
REVERT: A  297 TYR cc_start: 0.8579 (t80) cc_final: 0.8344 (t80)
REVERT: A  299 TYR cc_start: 0.6613 (t80) cc_final: 0.6263 (t80)
REVERT: A  413 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.6197 (t80)
REVERT: A  478 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7476 (tm)
REVERT: A  482 PHE cc_start: 0.6745 (m-10) cc_final: 0.6488 (m-80)
REVERT: A  522 TRP cc_start: 0.7438 (t-100) cc_final: 0.5567 (t60)
REVERT: B  125 ARG cc_start: 0.6506 (pmt170) cc_final: 0.5991 (ptt180)
REVERT: B  151 LEU cc_start: 0.8777 (tt) cc_final: 0.8328 (mt)
REVERT: B  413 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6276 (t80)
REVERT: B  522 TRP cc_start: 0.7434 (t-100) cc_final: 0.5349 (t60)
  outliers start: 45
  outliers final: 39
  residues processed: 167
  average time/residue: 0.0565
  time to fit residues: 13.5769
Evaluate side-chains
  168 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 125
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  190 ILE
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  411 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 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  190 ILE
Chi-restraints excluded: chain B residue  201 PHE
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  390 ASN
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  413 TYR
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 53 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.9380

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.214094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.192597 restraints weight = 7725.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.195719 restraints weight = 4973.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.197726 restraints weight = 3708.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.198948 restraints weight = 3056.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.199993 restraints weight = 2699.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6780  Z= 0.157
  Angle     :  0.687  12.820   9272  Z= 0.334
  Chirality :  0.042   0.182   1022
  Planarity :  0.005   0.042   1100
  Dihedral  :  5.574  47.200   1010
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 21.25 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.31), residues: 782
  helix:  0.52 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.18 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 219 
 TYR   0.019   0.001   TYR A 210 
 PHE   0.021   0.001   PHE B 398 
 TRP   0.008   0.001   TRP A 188 
 HIS   0.009   0.002   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6780)
  covalent geometry    : angle       0.68682 ( 9272)
  hydrogen bonds       : bond        0.03921 (  472)
  hydrogen bonds       : angle       5.68969 ( 1416)

*********************** 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
  172 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 127
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.6098 (ptt-90) cc_final: 0.5565 (ptt180)
REVERT: A  212 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7597 (mttt)
REVERT: A  273 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6400 (mt-10)
REVERT: A  297 TYR cc_start: 0.8592 (t80) cc_final: 0.8372 (t80)
REVERT: A  413 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.6115 (t80)
REVERT: A  478 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7500 (tm)
REVERT: A  522 TRP cc_start: 0.7477 (t-100) cc_final: 0.5620 (t60)
REVERT: B  125 ARG cc_start: 0.6496 (pmt170) cc_final: 0.5976 (ptt180)
REVERT: B  151 LEU cc_start: 0.8775 (tt) cc_final: 0.8318 (mt)
REVERT: B  413 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.6302 (t80)
REVERT: B  522 TRP cc_start: 0.7438 (t-100) cc_final: 0.5342 (t60)
  outliers start: 45
  outliers final: 38
  residues processed: 162
  average time/residue: 0.0576
  time to fit residues: 13.3997
Evaluate side-chains
  169 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 127
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
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  190 ILE
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  411 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 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  190 ILE
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  390 ASN
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  413 TYR
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 29 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    0.1980
   chunk 54 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0870
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5558

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.217898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.196481 restraints weight = 7633.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.199535 restraints weight = 4899.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.201396 restraints weight = 3679.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.202991 restraints weight = 3060.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.203455 restraints weight = 2664.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.4311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6780  Z= 0.135
  Angle     :  0.674  12.728   9272  Z= 0.326
  Chirality :  0.042   0.176   1022
  Planarity :  0.005   0.043   1100
  Dihedral  :  5.394  49.860   1010
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 23.09 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.31), residues: 782
  helix:  0.66 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -2.92 (0.49), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 219 
 TYR   0.019   0.001   TYR A 210 
 PHE   0.021   0.001   PHE A 398 
 TRP   0.009   0.001   TRP A 427 
 HIS   0.009   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6780)
  covalent geometry    : angle       0.67367 ( 9272)
  hydrogen bonds       : bond        0.03856 (  472)
  hydrogen bonds       : angle       5.59585 ( 1416)

********************** 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
  166 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.5942 (ptt-90) cc_final: 0.5370 (ptt180)
REVERT: A  212 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7572 (mttt)
REVERT: A  273 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6433 (mt-10)
REVERT: A  297 TYR cc_start: 0.8529 (t80) cc_final: 0.8295 (t80)
REVERT: A  413 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.6095 (t80)
REVERT: A  522 TRP cc_start: 0.7362 (t-100) cc_final: 0.5450 (t60)
REVERT: B  125 ARG cc_start: 0.6316 (pmt170) cc_final: 0.5748 (ptt180)
REVERT: B  413 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.6181 (t80)
REVERT: B  522 TRP cc_start: 0.7406 (t-100) cc_final: 0.5288 (t60)
  outliers start: 33
  outliers final: 26
  residues processed: 159
  average time/residue: 0.0558
  time to fit residues: 12.7754
Evaluate side-chains
  155 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  467 CYS
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  190 ILE
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  379 LEU
Chi-restraints excluded: chain B residue  380 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  413 TYR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  467 CYS
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0270
   chunk 42 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS
B 205 HIS
B 215 HIS
B 390 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.212488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.190593 restraints weight = 7631.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.193830 restraints weight = 4895.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.195583 restraints weight = 3677.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.197313 restraints weight = 3083.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.198128 restraints weight = 2676.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6780  Z= 0.135
  Angle     :  0.667  13.046   9272  Z= 0.323
  Chirality :  0.042   0.176   1022
  Planarity :  0.005   0.046   1100
  Dihedral  :  5.376  51.474   1010
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 22.02 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.31), residues: 782
  helix:  0.74 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -2.87 (0.49), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 219 
 TYR   0.019   0.001   TYR A 210 
 PHE   0.029   0.001   PHE A 482 
 TRP   0.010   0.001   TRP A 427 
 HIS   0.010   0.002   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6780)
  covalent geometry    : angle       0.66652 ( 9272)
  hydrogen bonds       : bond        0.03781 (  472)
  hydrogen bonds       : angle       5.51969 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1046.34 seconds
wall clock time: 18 minutes 46.16 seconds (1126.16 seconds total)