Starting phenix.real_space_refine
on Tue Jan 14 00:05:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.025
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      25      5.16       5
     C    2995      2.51       5
     N     747      2.21       5
     O     804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 4571
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3651
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 16, 'TRANS': 454}
    Chain: "B"
      Number of atoms: 920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 920
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
  Time building chain proxies: 3.16, per 1000 atoms: 0.69
  Number of scatterers: 4571
  At special positions: 0
  Unit cell: (100.254, 72.912, 88.536, 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      25     16.00
     O     804      8.00
     N     747      7.00
     C    2995      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 542.8 milliseconds
  

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1074

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 3 sheets defined
      70.1% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 102
    Processing helix  chain 'A' and resid 104 through 112
      removed outlier: 3.823A  pdb=" N   LEU A 108 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A 111 " --> pdb=" O   PHE A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 128
      removed outlier: 3.623A  pdb=" N   SER A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 158
      removed outlier: 3.577A  pdb=" N   LEU A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 168
    Processing helix  chain 'A' and resid 171 through 205
      removed outlier: 3.578A  pdb=" N   ALA A 185 " --> pdb=" O   MET A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.866A  pdb=" N   THR A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 232
      removed outlier: 3.728A  pdb=" N   THR A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 259
    Processing helix  chain 'A' and resid 261 through 271
    Processing helix  chain 'A' and resid 278 through 293
    Processing helix  chain 'A' and resid 296 through 308
      removed outlier: 3.660A  pdb=" N   ARG A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 350
      removed outlier: 4.011A  pdb=" N   VAL A 318 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG A 319 " --> pdb=" O   LYS A 315 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU A 320 " --> pdb=" O   GLN A 316 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ALA A 350 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 367
      removed outlier: 3.603A  pdb=" N   VAL A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 430
      Proline residue:  A 398  - end of helix
      removed outlier: 3.739A  pdb=" N   LEU A 401 " --> pdb=" O   GLY A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 459
      removed outlier: 3.692A  pdb=" N   ILE A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      removed outlier: 3.688A  pdb=" N   LEU A 454 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 478
      removed outlier: 3.867A  pdb=" N   ASN A 468 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASP A 469 " --> pdb=" O   THR A 465 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 482
    Processing helix  chain 'A' and resid 483 through 490
      removed outlier: 3.640A  pdb=" N   LEU A 487 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 497
    Processing helix  chain 'A' and resid 502 through 532
      removed outlier: 3.645A  pdb=" N   VAL A 525 " --> pdb=" O   MET A 521 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 526 " --> pdb=" O   TYR A 522 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU A 531 " --> pdb=" O   TYR A 527 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY A 532 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 562
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.628A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.857A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER B  25 " --> pdb=" O   GLN B   3 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.462A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   SER B 120 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS B  99 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   GLY B  33 " --> pdb=" O   LYS B  99 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ARG B  38 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   GLY B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.462A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   SER B 120 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL B  98 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   TYR B 110 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ASP B 100 " --> pdb=" O   TYR B 108 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 1.40 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: 1421
        1.34 -     1.46: 1181
        1.46 -     1.58: 2040
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 4681
  Sorted by residual:
  bond pdb=" N   GLY B  16 "
       pdb=" CA  GLY B  16 "
    ideal  model  delta    sigma   weight residual
    1.444  1.474 -0.030 9.60e-03 1.09e+04 9.47e+00
  bond pdb=" N   ARG B  19 "
       pdb=" CA  ARG B  19 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.25e-02 6.40e+03 7.17e+00
  bond pdb=" CA  SER A 414 "
       pdb=" CB  SER A 414 "
    ideal  model  delta    sigma   weight residual
    1.530  1.489  0.041 1.57e-02 4.06e+03 6.70e+00
  bond pdb=" N   LEU B  20 "
       pdb=" CA  LEU B  20 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.31e-02 5.83e+03 6.67e+00
  bond pdb=" CA  SER A 476 "
       pdb=" CB  SER A 476 "
    ideal  model  delta    sigma   weight residual
    1.528  1.488  0.040 1.66e-02 3.63e+03 5.93e+00
  ... (remaining 4676 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 6172
        1.90 -     3.79: 138
        3.79 -     5.69: 44
        5.69 -     7.59: 7
        7.59 -     9.48: 7
  Bond angle restraints: 6368
  Sorted by residual:
  angle pdb=" N   ILE B  51 "
        pdb=" CA  ILE B  51 "
        pdb=" C   ILE B  51 "
      ideal   model   delta    sigma   weight residual
     111.88  104.09    7.79 1.06e+00 8.90e-01 5.41e+01
  angle pdb=" N   GLY B  10 "
        pdb=" CA  GLY B  10 "
        pdb=" C   GLY B  10 "
      ideal   model   delta    sigma   weight residual
     110.46  117.17   -6.71 1.43e+00 4.89e-01 2.20e+01
  angle pdb=" CA  THR A 103 "
        pdb=" CB  THR A 103 "
        pdb=" OG1 THR A 103 "
      ideal   model   delta    sigma   weight residual
     109.60  103.33    6.27 1.50e+00 4.44e-01 1.74e+01
  angle pdb=" N   SER A 476 "
        pdb=" CA  SER A 476 "
        pdb=" C   SER A 476 "
      ideal   model   delta    sigma   weight residual
     111.82  107.22    4.60 1.16e+00 7.43e-01 1.57e+01
  angle pdb=" N   GLN A 478 "
        pdb=" CA  GLN A 478 "
        pdb=" C   GLN A 478 "
      ideal   model   delta    sigma   weight residual
     113.15  108.97    4.18 1.19e+00 7.06e-01 1.23e+01
  ... (remaining 6363 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.07: 2202
       15.07 -    30.14: 327
       30.14 -    45.21: 131
       45.21 -    60.27: 42
       60.27 -    75.34: 2
  Dihedral angle restraints: 2704
    sinusoidal: 1015
      harmonic: 1689
  Sorted by residual:
  dihedral pdb=" CA  ASN B  52 "
           pdb=" C   ASN B  52 "
           pdb=" N   SER B  53 "
           pdb=" CA  SER B  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.30  -17.70     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  TYR B  80 "
           pdb=" C   TYR B  80 "
           pdb=" N   LEU B  81 "
           pdb=" CA  LEU B  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.68   16.32     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" N   TYR A 231 "
           pdb=" CA  TYR A 231 "
           pdb=" CB  TYR A 231 "
           pdb=" CG  TYR A 231 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.14  -59.86     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 2701 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 525
       0.040 -    0.079: 152
       0.079 -    0.119: 45
       0.119 -    0.159: 8
       0.159 -    0.199: 5
  Chirality restraints: 735
  Sorted by residual:
  chirality pdb=" CA  ILE B  51 "
            pdb=" N   ILE B  51 "
            pdb=" C   ILE B  51 "
            pdb=" CB  ILE B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" CB  ILE B  51 "
            pdb=" CA  ILE B  51 "
            pdb=" CG1 ILE B  51 "
            pdb=" CG2 ILE B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.20 2.00e-01 2.50e+01 9.51e-01
  chirality pdb=" CA  CYS B  22 "
            pdb=" N   CYS B  22 "
            pdb=" C   CYS B  22 "
            pdb=" CB  CYS B  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.01e-01
  ... (remaining 732 not shown)

  Planarity restraints: 792
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 475 "    0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   GLN A 475 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   GLN A 475 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER A 476 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 301 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   HIS A 301 "    0.030 2.00e-02 2.50e+03
        pdb=" O   HIS A 301 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER A 302 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 104 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.62e+00
        pdb=" N   PRO A 105 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 105 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 105 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 789 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1226
        2.79 -     3.32: 4704
        3.32 -     3.85: 7890
        3.85 -     4.37: 8410
        4.37 -     4.90: 14273
  Nonbonded interactions: 36503
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 377 "
            pdb=" OG  SER A 379 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   SER B  85 "
            pdb=" OG  SER B  85 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   GLY A 353 "
            pdb=" ND2 ASN B  74 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   LEU A 487 "
            pdb=" OG  SER A 491 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" N   GLN B  13 "
            pdb=" OE1 GLN B  13 "
     model   vdw
     2.324 3.120
  ... (remaining 36498 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.600
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
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      :  0.004   0.063   4681  Z= 0.255
  Angle     :  0.798   9.483   6368  Z= 0.440
  Chirality :  0.043   0.199    735
  Planarity :  0.004   0.040    792
  Dihedral  : 17.495  75.343   1624
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 40.78 %
    Favored  : 56.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.35), residues: 587
  helix:  1.62 (0.27), residues: 379
  sheet: -0.29 (0.59), residues: 65
  loop : -1.68 (0.49), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  36 
 HIS   0.004   0.001   HIS A 301 
 PHE   0.015   0.001   PHE A 347 
 TYR   0.016   0.001   TYR B  95 
 ARG   0.007   0.001   ARG B  67 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8587 (tm-30)
REVERT: A  347 PHE cc_start: 0.8947 (m-80) cc_final: 0.8452 (t80)
REVERT: A  478 GLN cc_start: 0.9334 (pp30) cc_final: 0.8968 (pp30)
REVERT: A  521 MET cc_start: 0.8459 (ppp) cc_final: 0.8166 (ppp)
REVERT: A  537 TYR cc_start: 0.3868 (OUTLIER) cc_final: 0.1977 (t80)
REVERT: B   21 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8155 (p)
REVERT: B   80 TYR cc_start: 0.8030 (m-10) cc_final: 0.7644 (m-10)
REVERT: B   99 LYS cc_start: 0.8723 (mmmm) cc_final: 0.7959 (mmtm)
  outliers start: 15
  outliers final: 6
  residues processed: 129
  average time/residue: 0.1307
  time to fit residues: 22.5664
Evaluate side-chains
  123 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  231 TYR
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.131101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.108995 restraints weight = 9681.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.112234 restraints weight = 5027.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.114423 restraints weight = 3086.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4681  Z= 0.255
  Angle     :  0.650   8.882   6368  Z= 0.336
  Chirality :  0.041   0.201    735
  Planarity :  0.004   0.044    792
  Dihedral  :  6.763  57.039    653
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  8.81 %
    Allowed  : 31.35 %
    Favored  : 59.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.34), residues: 587
  helix:  1.61 (0.26), residues: 388
  sheet: -0.40 (0.69), residues: 57
  loop : -1.78 (0.46), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 179 
 HIS   0.002   0.001   HIS A 301 
 PHE   0.017   0.001   PHE A 347 
 TYR   0.010   0.001   TYR B 103 
 ARG   0.005   0.001   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ASP cc_start: 0.8494 (p0) cc_final: 0.7965 (p0)
REVERT: A  153 ARG cc_start: 0.7582 (mtp180) cc_final: 0.7099 (mtp180)
REVERT: A  269 MET cc_start: 0.7758 (ttm) cc_final: 0.7532 (ttp)
REVERT: A  283 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8649 (tm-30)
REVERT: A  347 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8766 (t80)
REVERT: A  395 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8475 (m-10)
REVERT: A  435 TRP cc_start: 0.7711 (OUTLIER) cc_final: 0.7319 (m-10)
REVERT: A  537 TYR cc_start: 0.4009 (OUTLIER) cc_final: 0.2013 (t80)
REVERT: B   20 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8592 (tm)
REVERT: B   99 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8488 (mmmm)
  outliers start: 43
  outliers final: 28
  residues processed: 152
  average time/residue: 0.1224
  time to fit residues: 24.8746
Evaluate side-chains
  144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue  118 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.131134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.108947 restraints weight = 9855.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112149 restraints weight = 5113.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.114320 restraints weight = 3153.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4681  Z= 0.203
  Angle     :  0.627   9.935   6368  Z= 0.316
  Chirality :  0.040   0.223    735
  Planarity :  0.004   0.043    792
  Dihedral  :  6.291  56.475    650
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 30.53 %
    Favored  : 62.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.35), residues: 587
  helix:  1.70 (0.26), residues: 387
  sheet: -0.53 (0.68), residues: 57
  loop : -1.72 (0.47), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 179 
 HIS   0.005   0.001   HIS A 301 
 PHE   0.015   0.001   PHE A 347 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.004   0.000   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7149 (mtp180)
REVERT: A  225 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7655 (t80)
REVERT: A  283 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8613 (tm-30)
REVERT: A  347 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8757 (t80)
REVERT: A  472 ASN cc_start: 0.9232 (t0) cc_final: 0.8949 (t0)
REVERT: A  496 MET cc_start: 0.8785 (tpp) cc_final: 0.8465 (tpp)
REVERT: A  537 TYR cc_start: 0.3874 (OUTLIER) cc_final: 0.2030 (t80)
REVERT: B   20 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8438 (tm)
REVERT: B   80 TYR cc_start: 0.8004 (m-10) cc_final: 0.7528 (m-10)
REVERT: B   99 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8490 (mmmm)
  outliers start: 35
  outliers final: 22
  residues processed: 146
  average time/residue: 0.1238
  time to fit residues: 24.2523
Evaluate side-chains
  142 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0370
   chunk 57 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.132392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.109871 restraints weight = 9968.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.113214 restraints weight = 5160.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.115534 restraints weight = 3156.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4681  Z= 0.197
  Angle     :  0.626  13.723   6368  Z= 0.314
  Chirality :  0.040   0.225    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.792  58.400    647
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  7.79 %
    Allowed  : 30.12 %
    Favored  : 62.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.35), residues: 587
  helix:  1.77 (0.26), residues: 387
  sheet: -0.48 (0.67), residues: 57
  loop : -1.65 (0.48), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.017   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.004   0.000   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7202 (mtp180)
REVERT: A  183 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8589 (mp0)
REVERT: A  192 GLN cc_start: 0.8547 (pt0) cc_final: 0.7854 (mt0)
REVERT: A  225 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7670 (t80)
REVERT: A  283 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8612 (tm-30)
REVERT: A  431 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7380 (pp)
REVERT: A  472 ASN cc_start: 0.9220 (t0) cc_final: 0.8985 (t0)
REVERT: A  496 MET cc_start: 0.8884 (tpp) cc_final: 0.8523 (tpp)
REVERT: A  521 MET cc_start: 0.8412 (ppp) cc_final: 0.7933 (ppp)
REVERT: A  537 TYR cc_start: 0.3841 (OUTLIER) cc_final: 0.2030 (t80)
REVERT: B   20 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (tm)
REVERT: B   80 TYR cc_start: 0.8038 (m-10) cc_final: 0.7540 (m-10)
REVERT: B   99 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8490 (mmmm)
REVERT: B  115 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7169 (t)
  outliers start: 38
  outliers final: 19
  residues processed: 149
  average time/residue: 0.1249
  time to fit residues: 25.2528
Evaluate side-chains
  144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue  115 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.132042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.109158 restraints weight = 10218.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.112437 restraints weight = 5260.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.114707 restraints weight = 3224.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4681  Z= 0.197
  Angle     :  0.637  13.733   6368  Z= 0.316
  Chirality :  0.040   0.180    735
  Planarity :  0.004   0.042    792
  Dihedral  :  5.848  59.871    647
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 31.56 %
    Favored  : 62.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.35), residues: 587
  helix:  1.73 (0.26), residues: 387
  sheet: -0.59 (0.66), residues: 57
  loop : -1.60 (0.48), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 179 
 HIS   0.005   0.001   HIS A 301 
 PHE   0.018   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.004   0.000   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.7720 (mtp180) cc_final: 0.7317 (mtp180)
REVERT: A  192 GLN cc_start: 0.8552 (pt0) cc_final: 0.7879 (mt0)
REVERT: A  225 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7650 (t80)
REVERT: A  283 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8564 (tm-30)
REVERT: A  472 ASN cc_start: 0.9157 (t0) cc_final: 0.8918 (t0)
REVERT: A  488 THR cc_start: 0.8766 (m) cc_final: 0.8523 (p)
REVERT: A  496 MET cc_start: 0.8864 (tpp) cc_final: 0.8530 (tpp)
REVERT: A  537 TYR cc_start: 0.3897 (OUTLIER) cc_final: 0.1999 (t80)
REVERT: B   11 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8204 (mp)
REVERT: B   20 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8683 (tm)
REVERT: B   80 TYR cc_start: 0.7995 (m-10) cc_final: 0.7514 (m-10)
REVERT: B   99 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8553 (mmmm)
  outliers start: 30
  outliers final: 19
  residues processed: 144
  average time/residue: 0.1285
  time to fit residues: 24.6441
Evaluate side-chains
  139 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 22 optimal weight:    0.1980
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 297 ASN
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.132961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.110113 restraints weight = 9944.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113446 restraints weight = 5130.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.115735 restraints weight = 3149.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4681  Z= 0.185
  Angle     :  0.654  14.754   6368  Z= 0.322
  Chirality :  0.041   0.250    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.812  58.421    647
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 32.79 %
    Favored  : 61.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.35), residues: 587
  helix:  1.80 (0.26), residues: 389
  sheet: -0.27 (0.69), residues: 52
  loop : -1.56 (0.49), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.017   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.003   0.000   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8752 (m-80) cc_final: 0.8455 (m-80)
REVERT: A  153 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7509 (mtp180)
REVERT: A  192 GLN cc_start: 0.8548 (pt0) cc_final: 0.7894 (mt0)
REVERT: A  225 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7585 (t80)
REVERT: A  283 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8543 (tm-30)
REVERT: A  472 ASN cc_start: 0.9149 (t0) cc_final: 0.8910 (t0)
REVERT: A  488 THR cc_start: 0.8764 (m) cc_final: 0.8518 (p)
REVERT: A  496 MET cc_start: 0.8833 (tpp) cc_final: 0.8523 (tpp)
REVERT: A  537 TYR cc_start: 0.3853 (OUTLIER) cc_final: 0.1991 (t80)
REVERT: B   11 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8237 (mp)
REVERT: B   20 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8726 (tm)
REVERT: B   59 TYR cc_start: 0.4648 (OUTLIER) cc_final: 0.3941 (p90)
REVERT: B   80 TYR cc_start: 0.7941 (m-10) cc_final: 0.7478 (m-10)
REVERT: B   99 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8572 (mmmm)
  outliers start: 29
  outliers final: 20
  residues processed: 139
  average time/residue: 0.1415
  time to fit residues: 26.0741
Evaluate side-chains
  134 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue   59 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0870
   chunk 35 optimal weight:    0.0970
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.111195 restraints weight = 9833.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114498 restraints weight = 4996.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.116780 restraints weight = 3042.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4681  Z= 0.196
  Angle     :  0.673  14.220   6368  Z= 0.333
  Chirality :  0.041   0.222    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.758  57.343    647
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 32.38 %
    Favored  : 61.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.35), residues: 587
  helix:  1.83 (0.27), residues: 390
  sheet: -0.41 (0.66), residues: 52
  loop : -1.52 (0.50), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.021   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.010   0.000   ARG B  38 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8766 (m-80) cc_final: 0.8530 (m-80)
REVERT: A  153 ARG cc_start: 0.7747 (mtp180) cc_final: 0.7309 (mtp180)
REVERT: A  192 GLN cc_start: 0.8513 (pt0) cc_final: 0.7878 (mt0)
REVERT: A  283 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: A  472 ASN cc_start: 0.9187 (t0) cc_final: 0.8950 (t0)
REVERT: A  488 THR cc_start: 0.8734 (m) cc_final: 0.8508 (p)
REVERT: A  496 MET cc_start: 0.8854 (tpp) cc_final: 0.8540 (tpp)
REVERT: A  537 TYR cc_start: 0.3807 (OUTLIER) cc_final: 0.1989 (t80)
REVERT: B   11 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8159 (mp)
REVERT: B   46 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8184 (pp20)
REVERT: B   80 TYR cc_start: 0.7939 (m-10) cc_final: 0.7438 (m-10)
REVERT: B   99 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8466 (mmmm)
  outliers start: 29
  outliers final: 21
  residues processed: 145
  average time/residue: 0.1323
  time to fit residues: 25.5762
Evaluate side-chains
  140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   54 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 54 optimal weight:    0.2980
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.133318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.110315 restraints weight = 9889.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.113620 restraints weight = 5177.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.115865 restraints weight = 3212.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4681  Z= 0.215
  Angle     :  0.710  16.620   6368  Z= 0.352
  Chirality :  0.043   0.276    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.819  59.960    647
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 32.99 %
    Favored  : 61.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.35), residues: 587
  helix:  1.83 (0.27), residues: 390
  sheet: -0.52 (0.65), residues: 52
  loop : -1.48 (0.49), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.020   0.001   TYR B  95 
 ARG   0.007   0.001   ARG B  19 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8769 (m-80) cc_final: 0.8446 (m-80)
REVERT: A  153 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7339 (mtp180)
REVERT: A  192 GLN cc_start: 0.8540 (pt0) cc_final: 0.7877 (mt0)
REVERT: A  283 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8555 (tm-30)
REVERT: A  472 ASN cc_start: 0.9141 (t0) cc_final: 0.8902 (t0)
REVERT: A  496 MET cc_start: 0.8863 (tpp) cc_final: 0.8559 (tpp)
REVERT: A  537 TYR cc_start: 0.3846 (OUTLIER) cc_final: 0.1997 (t80)
REVERT: B   11 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8109 (mp)
REVERT: B   46 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8168 (pp20)
  outliers start: 29
  outliers final: 23
  residues processed: 136
  average time/residue: 0.1285
  time to fit residues: 23.6691
Evaluate side-chains
  140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue   65 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0070
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.110822 restraints weight = 9857.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.114158 restraints weight = 5173.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.116274 restraints weight = 3214.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4681  Z= 0.210
  Angle     :  0.720  15.832   6368  Z= 0.355
  Chirality :  0.043   0.248    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.751  59.773    647
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 33.20 %
    Favored  : 61.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.35), residues: 587
  helix:  1.80 (0.26), residues: 391
  sheet: -0.35 (0.66), residues: 52
  loop : -1.51 (0.49), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 179 
 HIS   0.003   0.000   HIS A 301 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.007   0.001   ARG B  19 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8735 (m-80) cc_final: 0.8439 (m-80)
REVERT: A  153 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7381 (mtp180)
REVERT: A  192 GLN cc_start: 0.8538 (pt0) cc_final: 0.7874 (mt0)
REVERT: A  283 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8565 (tm-30)
REVERT: A  496 MET cc_start: 0.8856 (tpp) cc_final: 0.8545 (tpp)
REVERT: A  537 TYR cc_start: 0.3812 (OUTLIER) cc_final: 0.1993 (t80)
REVERT: B   46 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8174 (pp20)
REVERT: B   80 TYR cc_start: 0.7834 (m-10) cc_final: 0.7498 (m-10)
REVERT: B   99 LYS cc_start: 0.8593 (mmmm) cc_final: 0.7712 (mmtm)
  outliers start: 26
  outliers final: 23
  residues processed: 135
  average time/residue: 0.1418
  time to fit residues: 25.5779
Evaluate side-chains
  141 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   65 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   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 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.133512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.110682 restraints weight = 9800.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.113893 restraints weight = 5153.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.116176 restraints weight = 3221.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   4681  Z= 0.219
  Angle     :  0.731  16.153   6368  Z= 0.360
  Chirality :  0.043   0.239    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.517  59.629    645
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 34.63 %
    Favored  : 60.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.35), residues: 587
  helix:  1.78 (0.27), residues: 391
  sheet: -0.34 (0.66), residues: 52
  loop : -1.47 (0.49), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 179 
 HIS   0.003   0.000   HIS A 301 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.007   0.001   ARG B  38 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8739 (m-80) cc_final: 0.8420 (m-80)
REVERT: A  153 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7598 (mtp180)
REVERT: A  192 GLN cc_start: 0.8596 (pt0) cc_final: 0.7921 (mt0)
REVERT: A  283 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8451 (tm-30)
REVERT: A  294 MET cc_start: 0.7966 (mtm) cc_final: 0.7364 (mtp)
REVERT: A  496 MET cc_start: 0.8867 (tpp) cc_final: 0.8526 (tpp)
REVERT: A  537 TYR cc_start: 0.3853 (OUTLIER) cc_final: 0.1985 (t80)
REVERT: B   46 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8141 (pp20)
REVERT: B   80 TYR cc_start: 0.7852 (m-10) cc_final: 0.7492 (m-10)
  outliers start: 23
  outliers final: 20
  residues processed: 131
  average time/residue: 0.1427
  time to fit residues: 24.5906
Evaluate side-chains
  132 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   46 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0010
   chunk 40 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 56 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.110538 restraints weight = 10052.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.113865 restraints weight = 5272.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.116212 restraints weight = 3276.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4681  Z= 0.217
  Angle     :  0.745  15.968   6368  Z= 0.368
  Chirality :  0.042   0.234    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.433  58.899    645
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 35.04 %
    Favored  : 60.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.35), residues: 587
  helix:  1.79 (0.27), residues: 390
  sheet: -0.40 (0.65), residues: 52
  loop : -1.39 (0.49), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 179 
 HIS   0.003   0.000   HIS A 301 
 PHE   0.014   0.001   PHE A 550 
 TYR   0.019   0.001   TYR B  95 
 ARG   0.008   0.001   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1573.96 seconds
wall clock time: 28 minutes 59.69 seconds (1739.69 seconds total)