Starting phenix.real_space_refine
on Mon Jun  9 21:19:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xzd_38793/06_2025/8xzd_38793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xzd_38793/06_2025/8xzd_38793.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xzd_38793/06_2025/8xzd_38793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xzd_38793/06_2025/8xzd_38793.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xzd_38793/06_2025/8xzd_38793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xzd_38793/06_2025/8xzd_38793.cif"
  }
  resolution = 3.47
  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=   0.003 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5736 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4122      2.51       5
     N    1070      2.21       5
     O    1206      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6436
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1550
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
    Chain: "A"
      Number of atoms: 4885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4885
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 29, 'TRANS': 566}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.10, per 1000 atoms: 0.79
  Number of scatterers: 6436
  At special positions: 0
  Unit cell: (73.83, 86.25, 120.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1206      8.00
     N    1070      7.00
     C    4122      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.50

  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: 1.70
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 378 "


  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      57.4% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.589A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN B 343 " --> pdb=" O   ASP B 339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 338 through 343'
    Processing helix  chain 'B' and resid 365 through 372
      removed outlier: 3.816A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   PHE B 371 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA B 372 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.702A  pdb=" N   TYR A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU A  38 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.664A  pdb=" N   LYS A  68 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.524A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.697A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 252
      removed outlier: 3.911A  pdb=" N   ASP A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLN A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.687A  pdb=" N   ASP A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   THR A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.709A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.512A  pdb=" N   PHE A 369 " --> pdb=" O   THR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 414
      removed outlier: 3.676A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 466
      removed outlier: 3.655A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   THR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.516A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 561
      removed outlier: 3.937A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU A 560 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY A 561 " --> pdb=" O   MET A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.669A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.689A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 358
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.746A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.450A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    873 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.67

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 1831
        1.33 -     1.46: 1880
        1.46 -     1.59: 2855
        1.59 -     1.72: 0
        1.72 -     1.86: 58
  Bond restraints: 6624
  Sorted by residual:
  bond pdb=" CA  GLN A 522 "
       pdb=" C   GLN A 522 "
    ideal  model  delta    sigma   weight residual
    1.524  1.449  0.075 1.27e-02 6.20e+03 3.47e+01
  bond pdb=" CA  TYR A 252 "
       pdb=" C   TYR A 252 "
    ideal  model  delta    sigma   weight residual
    1.523  1.465  0.058 1.00e-02 1.00e+04 3.38e+01
  bond pdb=" CA  ASN A 134 "
       pdb=" C   ASN A 134 "
    ideal  model  delta    sigma   weight residual
    1.526  1.461  0.065 1.14e-02 7.69e+03 3.25e+01
  bond pdb=" CA  TRP A 477 "
       pdb=" C   TRP A 477 "
    ideal  model  delta    sigma   weight residual
    1.524  1.457  0.067 1.27e-02 6.20e+03 2.77e+01
  bond pdb=" CA  TRP A 211 "
       pdb=" C   TRP A 211 "
    ideal  model  delta    sigma   weight residual
    1.524  1.459  0.064 1.23e-02 6.61e+03 2.75e+01
  ... (remaining 6619 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 8183
        2.61 -     5.23: 628
        5.23 -     7.84: 138
        7.84 -    10.45: 42
       10.45 -    13.07: 15
  Bond angle restraints: 9006
  Sorted by residual:
  angle pdb=" N   SER A 339 "
        pdb=" CA  SER A 339 "
        pdb=" C   SER A 339 "
      ideal   model   delta    sigma   weight residual
     111.40  124.47  -13.07 1.22e+00 6.72e-01 1.15e+02
  angle pdb=" N   TYR A 255 "
        pdb=" CA  TYR A 255 "
        pdb=" C   TYR A 255 "
      ideal   model   delta    sigma   weight residual
     111.36  122.70  -11.34 1.09e+00 8.42e-01 1.08e+02
  angle pdb=" N   ALA A 264 "
        pdb=" CA  ALA A 264 "
        pdb=" C   ALA A 264 "
      ideal   model   delta    sigma   weight residual
     111.28  122.10  -10.82 1.09e+00 8.42e-01 9.86e+01
  angle pdb=" N   GLY A 286 "
        pdb=" CA  GLY A 286 "
        pdb=" C   GLY A 286 "
      ideal   model   delta    sigma   weight residual
     112.73  124.63  -11.90 1.20e+00 6.94e-01 9.83e+01
  angle pdb=" N   GLU A  22 "
        pdb=" CA  GLU A  22 "
        pdb=" C   GLU A  22 "
      ideal   model   delta    sigma   weight residual
     111.07  100.92   10.15 1.07e+00 8.73e-01 9.00e+01
  ... (remaining 9001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 3398
       17.27 -    34.53: 353
       34.53 -    51.80: 93
       51.80 -    69.07: 42
       69.07 -    86.33: 8
  Dihedral angle restraints: 3894
    sinusoidal: 1565
      harmonic: 2329
  Sorted by residual:
  dihedral pdb=" N   ASN A 195 "
           pdb=" C   ASN A 195 "
           pdb=" CA  ASN A 195 "
           pdb=" CB  ASN A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.62  -13.82     0      2.50e+00 1.60e-01 3.05e+01
  dihedral pdb=" C   THR A  21 "
           pdb=" N   THR A  21 "
           pdb=" CA  THR A  21 "
           pdb=" CB  THR A  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -108.26  -13.74     0      2.50e+00 1.60e-01 3.02e+01
  dihedral pdb=" C   ASN A 195 "
           pdb=" N   ASN A 195 "
           pdb=" CA  ASN A 195 "
           pdb=" CB  ASN A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.97   13.37     0      2.50e+00 1.60e-01 2.86e+01
  ... (remaining 3891 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.137: 636
       0.137 -    0.274: 229
       0.274 -    0.411: 51
       0.411 -    0.547: 16
       0.547 -    0.684: 1
  Chirality restraints: 933
  Sorted by residual:
  chirality pdb=" CA  ASN A 195 "
            pdb=" N   ASN A 195 "
            pdb=" C   ASN A 195 "
            pdb=" CB  ASN A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.83    0.68 2.00e-01 2.50e+01 1.17e+01
  chirality pdb=" CA  LEU A 450 "
            pdb=" N   LEU A 450 "
            pdb=" C   LEU A 450 "
            pdb=" CB  LEU A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.43e+00
  chirality pdb=" CA  GLU A 145 "
            pdb=" N   GLU A 145 "
            pdb=" C   GLU A 145 "
            pdb=" CB  GLU A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.76e+00
  ... (remaining 930 not shown)

  Planarity restraints: 1168
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 410 "    0.020 2.00e-02 2.50e+03   3.99e-02 1.59e+01
        pdb=" C   ILE B 410 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   ILE B 410 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ALA B 411 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 234 "    0.050 5.00e-02 4.00e+02   7.53e-02 9.07e+00
        pdb=" N   PRO A 235 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  79 "   -0.014 2.00e-02 2.50e+03   2.90e-02 8.43e+00
        pdb=" C   LEU A  79 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LEU A  79 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ALA A  80 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1165 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 116
        2.62 -     3.19: 6205
        3.19 -     3.76: 9700
        3.76 -     4.33: 13152
        4.33 -     4.90: 21079
  Nonbonded interactions: 50252
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 393 "
            pdb=" OD1 ASN A 394 "
     model   vdw
     2.052 3.040
  nonbonded pdb=" CE2 TYR A 381 "
            pdb=" CE2 TYR A 385 "
     model   vdw
     2.314 3.640
  nonbonded pdb=" N   ASN A 397 "
            pdb=" O   ASN A 397 "
     model   vdw
     2.334 2.496
  nonbonded pdb=" O   SER A 122 "
            pdb=" OG1 THR A 125 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OD1 ASN B 477 "
            pdb=" N   LYS B 478 "
     model   vdw
     2.378 3.120
  ... (remaining 50247 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.510
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
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      :  0.019   0.468   6627  Z= 1.362
  Angle     :  1.706  22.501   9008  Z= 1.185
  Chirality :  0.152   0.684    933
  Planarity :  0.009   0.075   1168
  Dihedral  : 16.407  86.332   2397
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.05 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 13.06 %
    Favored  : 81.64 %
  Cbeta Deviations :  1.34 %
  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:  2.42 (0.29), residues: 787
  helix:  3.20 (0.25), residues: 370
  sheet:  0.73 (0.98), residues: 27
  loop :  0.10 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 163 
 HIS   0.013   0.002   HIS A 540 
 PHE   0.029   0.003   PHE B 375 
 TYR   0.031   0.003   TYR A 183 
 ARG   0.006   0.001   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30578 (  304)
  hydrogen bonds       : angle       7.74407 (  873)
  metal coordination   : bond        0.14965 (    2)
  SS BOND              : bond        0.46752 (    1)
  SS BOND              : angle      20.00262 (    2)
  covalent geometry    : bond        0.01796 ( 6624)
  covalent geometry    : angle       1.68015 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 311
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  500 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7572 (p)
REVERT: A   37 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6887 (mt-10)
REVERT: A   38 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7378 (pm20)
REVERT: A   39 LEU cc_start: 0.7957 (mp) cc_final: 0.7705 (mm)
REVERT: A   53 ASN cc_start: 0.5984 (t0) cc_final: 0.5609 (t0)
REVERT: A  181 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6675 (mt-10)
REVERT: A  208 GLU cc_start: 0.6843 (tt0) cc_final: 0.6634 (tt0)
REVERT: A  283 VAL cc_start: 0.8621 (t) cc_final: 0.8254 (m)
REVERT: A  336 PRO cc_start: 0.7962 (Cg_exo) cc_final: 0.7757 (Cg_endo)
REVERT: A  358 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7058 (tt)
REVERT: A  462 MET cc_start: 0.7460 (mtt) cc_final: 0.7251 (mtt)
REVERT: A  495 GLU cc_start: 0.7141 (tp30) cc_final: 0.6591 (mm-30)
REVERT: A  520 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7797 (mm)
REVERT: A  532 ILE cc_start: 0.8639 (mt) cc_final: 0.8057 (mt)
  outliers start: 37
  outliers final: 9
  residues processed: 325
  average time/residue: 0.2142
  time to fit residues: 87.6483
Evaluate side-chains
  267 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 253
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  489 GLU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  553 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0870
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B 414 GLN
B 450 ASN
B 474 GLN
A  89 GLN
A 228 HIS
A 330 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.124717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.105719 restraints weight = 11626.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.85
r_work: 0.3225 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6627  Z= 0.158
  Angle     :  0.618   6.408   9008  Z= 0.343
  Chirality :  0.044   0.142    933
  Planarity :  0.006   0.057   1168
  Dihedral  :  6.892  59.780    896
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.23 %
    Favored  : 76.76 %
  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:  1.86 (0.30), residues: 787
  helix:  2.64 (0.26), residues: 383
  sheet:  0.40 (0.96), residues: 27
  loop : -0.17 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 163 
 HIS   0.007   0.002   HIS A 265 
 PHE   0.017   0.002   PHE A 285 
 TYR   0.020   0.002   TYR B 451 
 ARG   0.005   0.001   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07262 (  304)
  hydrogen bonds       : angle       5.19682 (  873)
  metal coordination   : bond        0.00653 (    2)
  SS BOND              : bond        0.00929 (    1)
  SS BOND              : angle       1.24900 (    2)
  covalent geometry    : bond        0.00313 ( 6624)
  covalent geometry    : angle       0.61748 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 262
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8446 (tttm) cc_final: 0.8080 (tttm)
REVERT: B  380 TYR cc_start: 0.8189 (m-80) cc_final: 0.7757 (m-10)
REVERT: B  403 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7684 (ttm-80)
REVERT: B  460 ASN cc_start: 0.7835 (t0) cc_final: 0.7546 (t0)
REVERT: B  509 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7810 (mtt180)
REVERT: A   21 THR cc_start: 0.8234 (m) cc_final: 0.8022 (p)
REVERT: A   34 TYR cc_start: 0.7853 (m-10) cc_final: 0.7650 (m-80)
REVERT: A   35 GLU cc_start: 0.8462 (tp30) cc_final: 0.7890 (tp30)
REVERT: A   38 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7086 (pm20)
REVERT: A   87 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7473 (mt-10)
REVERT: A  121 ASN cc_start: 0.8462 (m-40) cc_final: 0.8249 (m-40)
REVERT: A  134 ASN cc_start: 0.8259 (t0) cc_final: 0.7998 (t0)
REVERT: A  142 LEU cc_start: 0.8385 (mt) cc_final: 0.8104 (mt)
REVERT: A  143 LEU cc_start: 0.7688 (tp) cc_final: 0.7403 (mt)
REVERT: A  152 MET cc_start: 0.8409 (mmt) cc_final: 0.8004 (mmt)
REVERT: A  153 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7725 (pp20)
REVERT: A  156 LYS cc_start: 0.8333 (mtmm) cc_final: 0.8106 (mtmm)
REVERT: A  160 GLU cc_start: 0.7870 (tt0) cc_final: 0.7667 (pt0)
REVERT: A  161 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.7987 (mtt-85)
REVERT: A  166 GLU cc_start: 0.7940 (tp30) cc_final: 0.7612 (tp30)
REVERT: A  174 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8222 (tppt)
REVERT: A  181 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7613 (mt-10)
REVERT: A  190 MET cc_start: 0.8284 (tmm) cc_final: 0.8005 (tmm)
REVERT: A  209 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7362 (mm-30)
REVERT: A  283 VAL cc_start: 0.8625 (t) cc_final: 0.8345 (m)
REVERT: A  312 GLU cc_start: 0.8112 (tt0) cc_final: 0.7868 (tm-30)
REVERT: A  322 ASN cc_start: 0.6291 (p0) cc_final: 0.5754 (p0)
REVERT: A  323 MET cc_start: 0.8477 (mmm) cc_final: 0.8211 (mmt)
REVERT: A  347 THR cc_start: 0.8472 (m) cc_final: 0.7843 (p)
REVERT: A  400 PHE cc_start: 0.8157 (m-10) cc_final: 0.7731 (m-80)
REVERT: A  439 LEU cc_start: 0.8407 (mt) cc_final: 0.8130 (mm)
REVERT: A  455 MET cc_start: 0.7916 (tmm) cc_final: 0.7521 (tmm)
REVERT: A  462 MET cc_start: 0.8554 (mtt) cc_final: 0.8275 (mtp)
REVERT: A  470 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7954 (mtpp)
REVERT: A  496 THR cc_start: 0.8468 (p) cc_final: 0.7930 (t)
REVERT: A  534 LYS cc_start: 0.8676 (mmtp) cc_final: 0.8407 (mmmm)
REVERT: A  552 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7979 (mm-40)
REVERT: A  553 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8305 (tptm)
REVERT: A  562 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8263 (ttpt)
REVERT: A  579 MET cc_start: 0.7802 (mtt) cc_final: 0.7596 (mtm)
REVERT: A  585 LEU cc_start: 0.8811 (mp) cc_final: 0.8522 (mm)
  outliers start: 21
  outliers final: 9
  residues processed: 271
  average time/residue: 0.2070
  time to fit residues: 71.1362
Evaluate side-chains
  250 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 239
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  276 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 586 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.122682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.103223 restraints weight = 11653.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.87
r_work: 0.3173 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6627  Z= 0.143
  Angle     :  0.548   6.538   9008  Z= 0.295
  Chirality :  0.042   0.145    933
  Planarity :  0.005   0.049   1168
  Dihedral  :  6.147  59.703    877
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.52 %
    Favored  : 76.18 %
  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:  1.78 (0.30), residues: 787
  helix:  2.52 (0.26), residues: 384
  sheet:  0.27 (0.93), residues: 25
  loop : -0.16 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.017   0.002   PHE A 230 
 TYR   0.023   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 600 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06160 (  304)
  hydrogen bonds       : angle       4.63913 (  873)
  metal coordination   : bond        0.00373 (    2)
  SS BOND              : bond        0.00854 (    1)
  SS BOND              : angle       1.42265 (    2)
  covalent geometry    : bond        0.00302 ( 6624)
  covalent geometry    : angle       0.54731 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 233
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8499 (tttm) cc_final: 0.8109 (tttm)
REVERT: B  403 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7704 (ttm-80)
REVERT: B  462 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8361 (mmmt)
REVERT: B  509 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7722 (mtt180)
REVERT: A   29 LEU cc_start: 0.8762 (mt) cc_final: 0.8362 (mp)
REVERT: A   30 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8351 (mm-30)
REVERT: A   34 TYR cc_start: 0.7871 (m-10) cc_final: 0.7453 (m-80)
REVERT: A   35 GLU cc_start: 0.8414 (tp30) cc_final: 0.8033 (tp30)
REVERT: A   38 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7111 (pm20)
REVERT: A   75 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7990 (tp30)
REVERT: A   81 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8560 (mmtp)
REVERT: A  134 ASN cc_start: 0.8312 (t0) cc_final: 0.8093 (t0)
REVERT: A  152 MET cc_start: 0.8518 (mmt) cc_final: 0.8081 (mmt)
REVERT: A  153 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7626 (pp20)
REVERT: A  155 SER cc_start: 0.8587 (t) cc_final: 0.7799 (t)
REVERT: A  161 ARG cc_start: 0.8469 (mtt-85) cc_final: 0.8018 (mtt-85)
REVERT: A  166 GLU cc_start: 0.7901 (tp30) cc_final: 0.7570 (tp30)
REVERT: A  188 ASN cc_start: 0.8426 (t0) cc_final: 0.8052 (t0)
REVERT: A  190 MET cc_start: 0.8323 (tmm) cc_final: 0.8079 (tmm)
REVERT: A  213 ASN cc_start: 0.8579 (m-40) cc_final: 0.8311 (t0)
REVERT: A  276 THR cc_start: 0.8818 (p) cc_final: 0.8594 (t)
REVERT: A  305 ARG cc_start: 0.8027 (mtp180) cc_final: 0.7791 (mtp180)
REVERT: A  312 GLU cc_start: 0.8087 (tt0) cc_final: 0.7837 (tm-30)
REVERT: A  322 ASN cc_start: 0.6374 (p0) cc_final: 0.5863 (p0)
REVERT: A  347 THR cc_start: 0.8466 (m) cc_final: 0.8012 (p)
REVERT: A  362 THR cc_start: 0.8641 (m) cc_final: 0.8253 (p)
REVERT: A  371 THR cc_start: 0.8536 (m) cc_final: 0.8287 (p)
REVERT: A  439 LEU cc_start: 0.8431 (mt) cc_final: 0.8175 (mm)
REVERT: A  455 MET cc_start: 0.8027 (tmm) cc_final: 0.7548 (tmm)
REVERT: A  462 MET cc_start: 0.8556 (mtt) cc_final: 0.8231 (mtp)
REVERT: A  496 THR cc_start: 0.8452 (p) cc_final: 0.7975 (t)
REVERT: A  527 GLU cc_start: 0.8461 (tt0) cc_final: 0.8111 (tp30)
REVERT: A  553 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8326 (mmtt)
REVERT: A  562 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8574 (ttmt)
  outliers start: 16
  outliers final: 9
  residues processed: 238
  average time/residue: 0.2034
  time to fit residues: 62.2581
Evaluate side-chains
  228 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 216
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain A residue  553 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    0.0040
   chunk 68 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0980
   chunk 67 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 483 ASN
A 586 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.125505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.106001 restraints weight = 11731.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.92
r_work: 0.3203 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6627  Z= 0.112
  Angle     :  0.508   5.657   9008  Z= 0.271
  Chirality :  0.040   0.151    933
  Planarity :  0.004   0.042   1168
  Dihedral  :  5.801  57.641    877
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 24.25 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.73 (0.30), residues: 787
  helix:  2.47 (0.26), residues: 385
  sheet:  0.81 (1.00), residues: 23
  loop : -0.22 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 165 
 HIS   0.003   0.000   HIS A 265 
 PHE   0.022   0.001   PHE B 497 
 TYR   0.020   0.001   TYR B 380 
 ARG   0.002   0.000   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  304)
  hydrogen bonds       : angle       4.44446 (  873)
  metal coordination   : bond        0.00141 (    2)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       1.30469 (    2)
  covalent geometry    : bond        0.00237 ( 6624)
  covalent geometry    : angle       0.50813 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 224
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8502 (tttm) cc_final: 0.8125 (tttm)
REVERT: B  403 ARG cc_start: 0.8141 (ttm170) cc_final: 0.7770 (ttm-80)
REVERT: B  462 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8292 (mmmt)
REVERT: A   30 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8327 (mm-30)
REVERT: A   34 TYR cc_start: 0.7812 (m-10) cc_final: 0.7449 (m-80)
REVERT: A   35 GLU cc_start: 0.8368 (tp30) cc_final: 0.7923 (tp30)
REVERT: A   38 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7123 (pm20)
REVERT: A   75 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8031 (tp30)
REVERT: A  115 ARG cc_start: 0.8845 (tpt170) cc_final: 0.8602 (tpt170)
REVERT: A  126 ILE cc_start: 0.8916 (mt) cc_final: 0.8596 (tt)
REVERT: A  150 ASP cc_start: 0.8171 (t0) cc_final: 0.7800 (t0)
REVERT: A  152 MET cc_start: 0.8546 (mmt) cc_final: 0.8224 (mmt)
REVERT: A  153 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7632 (pp20)
REVERT: A  161 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8093 (mtt-85)
REVERT: A  166 GLU cc_start: 0.7859 (tp30) cc_final: 0.7531 (tp30)
REVERT: A  188 ASN cc_start: 0.8420 (t0) cc_final: 0.8057 (t0)
REVERT: A  197 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7080 (mt-10)
REVERT: A  213 ASN cc_start: 0.8558 (m-40) cc_final: 0.8287 (t0)
REVERT: A  305 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7475 (ttt-90)
REVERT: A  312 GLU cc_start: 0.8041 (tt0) cc_final: 0.7767 (tm-30)
REVERT: A  322 ASN cc_start: 0.6381 (p0) cc_final: 0.5921 (p0)
REVERT: A  347 THR cc_start: 0.8475 (m) cc_final: 0.8083 (p)
REVERT: A  362 THR cc_start: 0.8534 (m) cc_final: 0.8200 (p)
REVERT: A  371 THR cc_start: 0.8426 (m) cc_final: 0.8171 (p)
REVERT: A  439 LEU cc_start: 0.8396 (mt) cc_final: 0.8132 (mm)
REVERT: A  455 MET cc_start: 0.8048 (tmm) cc_final: 0.7512 (tmm)
REVERT: A  462 MET cc_start: 0.8569 (mtt) cc_final: 0.8251 (mtp)
REVERT: A  496 THR cc_start: 0.8456 (p) cc_final: 0.8081 (t)
REVERT: A  527 GLU cc_start: 0.8423 (tt0) cc_final: 0.8205 (tp30)
REVERT: A  562 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8625 (ttmt)
  outliers start: 19
  outliers final: 11
  residues processed: 230
  average time/residue: 0.2052
  time to fit residues: 60.0744
Evaluate side-chains
  231 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 218
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  511 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0870
   chunk 73 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0980
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
B 417 ASN
A  63 ASN
A 228 HIS
A 325 GLN
A 586 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.121814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.102097 restraints weight = 11678.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.95
r_work: 0.3166 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.5311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6627  Z= 0.122
  Angle     :  0.518   8.154   9008  Z= 0.272
  Chirality :  0.040   0.141    933
  Planarity :  0.004   0.038   1168
  Dihedral  :  5.214  55.760    871
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 24.82 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.30), residues: 787
  helix:  2.49 (0.27), residues: 379
  sheet:  0.14 (0.99), residues: 27
  loop : -0.19 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  48 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.022   0.001   PHE B 497 
 TYR   0.022   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 600 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05061 (  304)
  hydrogen bonds       : angle       4.33998 (  873)
  metal coordination   : bond        0.00247 (    2)
  SS BOND              : bond        0.00175 (    1)
  SS BOND              : angle       1.27539 (    2)
  covalent geometry    : bond        0.00265 ( 6624)
  covalent geometry    : angle       0.51782 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 237
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  338 PHE cc_start: 0.7895 (m-80) cc_final: 0.7472 (m-80)
REVERT: B  356 LYS cc_start: 0.8549 (tttm) cc_final: 0.8169 (tttm)
REVERT: B  403 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7790 (ttm-80)
REVERT: B  408 SER cc_start: 0.8964 (m) cc_final: 0.8707 (t)
REVERT: B  462 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8298 (mmmt)
REVERT: A   35 GLU cc_start: 0.8408 (tp30) cc_final: 0.8050 (tp30)
REVERT: A   38 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7187 (pm20)
REVERT: A   75 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8095 (tp30)
REVERT: A  152 MET cc_start: 0.8592 (mmt) cc_final: 0.8258 (mmt)
REVERT: A  153 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7594 (pp20)
REVERT: A  161 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.8094 (mtt-85)
REVERT: A  162 LEU cc_start: 0.8343 (tp) cc_final: 0.8110 (tt)
REVERT: A  166 GLU cc_start: 0.7930 (tp30) cc_final: 0.7546 (tp30)
REVERT: A  188 ASN cc_start: 0.8393 (t0) cc_final: 0.8041 (t0)
REVERT: A  197 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7139 (mt-10)
REVERT: A  207 TYR cc_start: 0.8409 (m-80) cc_final: 0.8051 (m-80)
REVERT: A  213 ASN cc_start: 0.8513 (m-40) cc_final: 0.8245 (t0)
REVERT: A  312 GLU cc_start: 0.8089 (tt0) cc_final: 0.7817 (tm-30)
REVERT: A  322 ASN cc_start: 0.6223 (p0) cc_final: 0.5822 (p0)
REVERT: A  347 THR cc_start: 0.8497 (m) cc_final: 0.8099 (p)
REVERT: A  362 THR cc_start: 0.8522 (m) cc_final: 0.8166 (p)
REVERT: A  371 THR cc_start: 0.8481 (m) cc_final: 0.8147 (p)
REVERT: A  439 LEU cc_start: 0.8427 (mt) cc_final: 0.8149 (mm)
REVERT: A  455 MET cc_start: 0.8108 (tmm) cc_final: 0.7506 (tmm)
REVERT: A  496 THR cc_start: 0.8413 (p) cc_final: 0.8044 (t)
REVERT: A  553 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8236 (tptp)
REVERT: A  562 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8589 (ttmt)
  outliers start: 20
  outliers final: 16
  residues processed: 244
  average time/residue: 0.2043
  time to fit residues: 65.3493
Evaluate side-chains
  250 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 232
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  483 ASN
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  553 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.118833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098931 restraints weight = 11564.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.92
r_work: 0.3118 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.5546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6627  Z= 0.167
  Angle     :  0.554   8.835   9008  Z= 0.295
  Chirality :  0.042   0.217    933
  Planarity :  0.005   0.054   1168
  Dihedral  :  5.262  57.046    871
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 26.11 %
    Favored  : 70.88 %
  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:  1.57 (0.30), residues: 787
  helix:  2.35 (0.26), residues: 386
  sheet:  0.72 (1.19), residues: 25
  loop : -0.34 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.026   0.002   PHE B 497 
 TYR   0.022   0.001   TYR A 385 
 ARG   0.014   0.001   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06015 (  304)
  hydrogen bonds       : angle       4.42389 (  873)
  metal coordination   : bond        0.00496 (    2)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       1.43750 (    2)
  covalent geometry    : bond        0.00365 ( 6624)
  covalent geometry    : angle       0.55320 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 239
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  338 PHE cc_start: 0.7931 (m-80) cc_final: 0.7515 (m-80)
REVERT: B  356 LYS cc_start: 0.8571 (tttm) cc_final: 0.8196 (tttm)
REVERT: B  400 PHE cc_start: 0.7707 (p90) cc_final: 0.7426 (p90)
REVERT: B  403 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7899 (ttm-80)
REVERT: B  408 SER cc_start: 0.9022 (m) cc_final: 0.8782 (t)
REVERT: B  444 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8388 (mtpp)
REVERT: B  462 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8331 (mmmt)
REVERT: A   35 GLU cc_start: 0.8434 (tp30) cc_final: 0.8165 (tp30)
REVERT: A   75 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8272 (tp30)
REVERT: A  153 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7684 (pp20)
REVERT: A  161 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.8078 (mtt-85)
REVERT: A  166 GLU cc_start: 0.7995 (tp30) cc_final: 0.7587 (tp30)
REVERT: A  188 ASN cc_start: 0.8381 (t0) cc_final: 0.8016 (t0)
REVERT: A  197 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7173 (mt-10)
REVERT: A  213 ASN cc_start: 0.8526 (m-40) cc_final: 0.8240 (t0)
REVERT: A  225 ASP cc_start: 0.7620 (m-30) cc_final: 0.7329 (m-30)
REVERT: A  312 GLU cc_start: 0.8040 (tt0) cc_final: 0.7838 (tm-30)
REVERT: A  322 ASN cc_start: 0.6332 (p0) cc_final: 0.5909 (p0)
REVERT: A  325 GLN cc_start: 0.8172 (mp10) cc_final: 0.7947 (mm-40)
REVERT: A  332 MET cc_start: 0.8367 (ttp) cc_final: 0.8148 (ptp)
REVERT: A  347 THR cc_start: 0.8480 (m) cc_final: 0.8068 (p)
REVERT: A  360 MET cc_start: 0.8267 (ttp) cc_final: 0.7878 (ttt)
REVERT: A  371 THR cc_start: 0.8556 (m) cc_final: 0.8164 (p)
REVERT: A  397 ASN cc_start: 0.8169 (p0) cc_final: 0.7960 (p0)
REVERT: A  439 LEU cc_start: 0.8500 (mt) cc_final: 0.8198 (mm)
REVERT: A  455 MET cc_start: 0.8187 (tmm) cc_final: 0.7965 (tmm)
REVERT: A  462 MET cc_start: 0.8699 (mtt) cc_final: 0.8412 (mtp)
REVERT: A  470 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7846 (ttmm)
REVERT: A  527 GLU cc_start: 0.8602 (tp30) cc_final: 0.8367 (tp30)
REVERT: A  553 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8269 (tptp)
REVERT: A  562 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8577 (ttmt)
  outliers start: 21
  outliers final: 16
  residues processed: 246
  average time/residue: 0.2085
  time to fit residues: 66.5955
Evaluate side-chains
  247 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 229
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain A residue  522 GLN
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  572 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0030
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 59 optimal weight:    0.2980
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
A  63 ASN
** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.122072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.102386 restraints weight = 11686.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.92
r_work: 0.3160 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.5746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6627  Z= 0.119
  Angle     :  0.553   9.476   9008  Z= 0.285
  Chirality :  0.041   0.201    933
  Planarity :  0.004   0.037   1168
  Dihedral  :  4.895  58.350    868
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.83 %
    Favored  : 70.30 %
  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:  1.65 (0.30), residues: 787
  helix:  2.46 (0.27), residues: 386
  sheet:  0.78 (1.18), residues: 25
  loop : -0.34 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.028   0.001   PHE B 497 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.005   0.000   ARG A 600 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04836 (  304)
  hydrogen bonds       : angle       4.36397 (  873)
  metal coordination   : bond        0.00204 (    2)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       1.39155 (    2)
  covalent geometry    : bond        0.00261 ( 6624)
  covalent geometry    : angle       0.55245 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 230
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  338 PHE cc_start: 0.7958 (m-80) cc_final: 0.7530 (m-80)
REVERT: B  356 LYS cc_start: 0.8603 (tttm) cc_final: 0.8204 (tttm)
REVERT: B  400 PHE cc_start: 0.7609 (p90) cc_final: 0.7293 (p90)
REVERT: B  403 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7853 (ttm-80)
REVERT: B  408 SER cc_start: 0.8951 (m) cc_final: 0.8725 (t)
REVERT: B  462 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8321 (mmmt)
REVERT: A   35 GLU cc_start: 0.8375 (tp30) cc_final: 0.8118 (tp30)
REVERT: A   75 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8288 (tp30)
REVERT: A  153 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7632 (pp20)
REVERT: A  161 ARG cc_start: 0.8522 (mtt-85) cc_final: 0.8098 (mtt-85)
REVERT: A  166 GLU cc_start: 0.7939 (tp30) cc_final: 0.7517 (tp30)
REVERT: A  188 ASN cc_start: 0.8374 (t0) cc_final: 0.8022 (t0)
REVERT: A  213 ASN cc_start: 0.8506 (m-40) cc_final: 0.8238 (t0)
REVERT: A  225 ASP cc_start: 0.7598 (m-30) cc_final: 0.7301 (m-30)
REVERT: A  312 GLU cc_start: 0.8058 (tt0) cc_final: 0.7767 (tm-30)
REVERT: A  322 ASN cc_start: 0.6214 (p0) cc_final: 0.5818 (p0)
REVERT: A  325 GLN cc_start: 0.8180 (mp10) cc_final: 0.7960 (mm-40)
REVERT: A  332 MET cc_start: 0.8290 (ttp) cc_final: 0.8062 (ptp)
REVERT: A  347 THR cc_start: 0.8462 (m) cc_final: 0.8070 (p)
REVERT: A  360 MET cc_start: 0.8313 (ttp) cc_final: 0.7912 (ttt)
REVERT: A  371 THR cc_start: 0.8377 (m) cc_final: 0.8046 (p)
REVERT: A  439 LEU cc_start: 0.8463 (mt) cc_final: 0.8182 (mm)
REVERT: A  455 MET cc_start: 0.8147 (tmm) cc_final: 0.7897 (tmm)
REVERT: A  462 MET cc_start: 0.8692 (mtt) cc_final: 0.8398 (mtp)
REVERT: A  474 MET cc_start: 0.7579 (mmm) cc_final: 0.7355 (mmm)
REVERT: A  553 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8245 (tptp)
REVERT: A  562 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8613 (ttmt)
  outliers start: 20
  outliers final: 14
  residues processed: 235
  average time/residue: 0.2042
  time to fit residues: 62.3863
Evaluate side-chains
  245 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 229
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  553 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 18 optimal weight:   30.0000
   chunk 5 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    0.1980
   chunk 41 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0170
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
A  63 ASN
A 134 ASN
** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.122303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102596 restraints weight = 11540.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.90
r_work: 0.3167 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6627  Z= 0.118
  Angle     :  0.556  10.218   9008  Z= 0.285
  Chirality :  0.041   0.241    933
  Planarity :  0.004   0.036   1168
  Dihedral  :  4.785  57.101    868
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 28.41 %
    Favored  : 69.30 %
  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:  1.66 (0.30), residues: 787
  helix:  2.46 (0.26), residues: 386
  sheet:  0.49 (0.92), residues: 35
  loop : -0.32 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.028   0.001   PHE B 497 
 TYR   0.023   0.001   TYR A 385 
 ARG   0.006   0.000   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04686 (  304)
  hydrogen bonds       : angle       4.37420 (  873)
  metal coordination   : bond        0.00156 (    2)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       1.39278 (    2)
  covalent geometry    : bond        0.00266 ( 6624)
  covalent geometry    : angle       0.55605 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 230
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  338 PHE cc_start: 0.7972 (m-80) cc_final: 0.7543 (m-80)
REVERT: B  356 LYS cc_start: 0.8601 (tttm) cc_final: 0.8198 (tttm)
REVERT: B  403 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7846 (ttm-80)
REVERT: B  409 GLN cc_start: 0.8280 (mt0) cc_final: 0.8052 (tt0)
REVERT: B  462 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8295 (mmmt)
REVERT: A   35 GLU cc_start: 0.8380 (tp30) cc_final: 0.8084 (tp30)
REVERT: A   75 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8281 (tp30)
REVERT: A  134 ASN cc_start: 0.8012 (t0) cc_final: 0.7771 (t0)
REVERT: A  153 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7607 (pp20)
REVERT: A  161 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.8068 (mtt-85)
REVERT: A  166 GLU cc_start: 0.7919 (tp30) cc_final: 0.7492 (tp30)
REVERT: A  188 ASN cc_start: 0.8362 (t0) cc_final: 0.8046 (t0)
REVERT: A  213 ASN cc_start: 0.8507 (m-40) cc_final: 0.8269 (t0)
REVERT: A  225 ASP cc_start: 0.7563 (m-30) cc_final: 0.7222 (m-30)
REVERT: A  312 GLU cc_start: 0.8039 (tt0) cc_final: 0.7767 (tm-30)
REVERT: A  322 ASN cc_start: 0.6292 (p0) cc_final: 0.5898 (p0)
REVERT: A  323 MET cc_start: 0.8298 (mmp) cc_final: 0.8010 (mmm)
REVERT: A  325 GLN cc_start: 0.8162 (mp10) cc_final: 0.7935 (mm-40)
REVERT: A  332 MET cc_start: 0.8290 (ttp) cc_final: 0.8079 (ptp)
REVERT: A  347 THR cc_start: 0.8446 (m) cc_final: 0.8055 (p)
REVERT: A  360 MET cc_start: 0.8274 (ttp) cc_final: 0.8073 (ttt)
REVERT: A  439 LEU cc_start: 0.8484 (mt) cc_final: 0.8192 (mm)
REVERT: A  455 MET cc_start: 0.8137 (tmm) cc_final: 0.7869 (tmm)
REVERT: A  462 MET cc_start: 0.8674 (mtt) cc_final: 0.8400 (mtp)
REVERT: A  474 MET cc_start: 0.7567 (mmm) cc_final: 0.7323 (mmm)
REVERT: A  553 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8235 (tptp)
REVERT: A  562 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8610 (ttmt)
REVERT: A  595 LEU cc_start: 0.8486 (mt) cc_final: 0.8153 (mp)
  outliers start: 16
  outliers final: 13
  residues processed: 234
  average time/residue: 0.1913
  time to fit residues: 58.2004
Evaluate side-chains
  243 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 228
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  553 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    0.2980
   chunk 59 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
A 228 HIS
** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.120327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.100580 restraints weight = 11740.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.94
r_work: 0.3135 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.5927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   6627  Z= 0.141
  Angle     :  0.570  10.513   9008  Z= 0.295
  Chirality :  0.041   0.274    933
  Planarity :  0.004   0.036   1168
  Dihedral  :  4.865  57.695    868
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 27.69 %
    Favored  : 69.44 %
  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:  1.60 (0.30), residues: 787
  helix:  2.43 (0.27), residues: 386
  sheet:  0.43 (1.07), residues: 27
  loop : -0.36 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.031   0.001   PHE B 497 
 TYR   0.022   0.001   TYR A 385 
 ARG   0.007   0.000   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05292 (  304)
  hydrogen bonds       : angle       4.41927 (  873)
  metal coordination   : bond        0.00345 (    2)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       1.42309 (    2)
  covalent geometry    : bond        0.00322 ( 6624)
  covalent geometry    : angle       0.56922 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 231
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  338 PHE cc_start: 0.7989 (m-80) cc_final: 0.7554 (m-80)
REVERT: B  356 LYS cc_start: 0.8636 (tttm) cc_final: 0.8259 (tttm)
REVERT: B  400 PHE cc_start: 0.7593 (p90) cc_final: 0.7321 (p90)
REVERT: B  403 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7870 (ttm-80)
REVERT: B  409 GLN cc_start: 0.8276 (mt0) cc_final: 0.8042 (tt0)
REVERT: B  444 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8410 (mtpp)
REVERT: B  462 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8304 (mmmt)
REVERT: A   35 GLU cc_start: 0.8411 (tp30) cc_final: 0.8112 (tp30)
REVERT: A   75 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8336 (tp30)
REVERT: A  134 ASN cc_start: 0.8185 (t0) cc_final: 0.7958 (t0)
REVERT: A  153 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7585 (pp20)
REVERT: A  161 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8204 (mtt-85)
REVERT: A  166 GLU cc_start: 0.7959 (tp30) cc_final: 0.7532 (tp30)
REVERT: A  188 ASN cc_start: 0.8377 (t0) cc_final: 0.8027 (t0)
REVERT: A  213 ASN cc_start: 0.8507 (m-40) cc_final: 0.8241 (t0)
REVERT: A  225 ASP cc_start: 0.7616 (m-30) cc_final: 0.7290 (m-30)
REVERT: A  312 GLU cc_start: 0.8080 (tt0) cc_final: 0.7747 (tm-30)
REVERT: A  322 ASN cc_start: 0.6245 (p0) cc_final: 0.5845 (p0)
REVERT: A  325 GLN cc_start: 0.8171 (mp10) cc_final: 0.7956 (mm-40)
REVERT: A  332 MET cc_start: 0.8292 (ttp) cc_final: 0.8063 (ptp)
REVERT: A  347 THR cc_start: 0.8451 (m) cc_final: 0.8011 (p)
REVERT: A  360 MET cc_start: 0.8237 (ttp) cc_final: 0.8012 (ttt)
REVERT: A  376 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8121 (tpp)
REVERT: A  455 MET cc_start: 0.8173 (tmm) cc_final: 0.7916 (tmm)
REVERT: A  462 MET cc_start: 0.8694 (mtt) cc_final: 0.8416 (mtp)
REVERT: A  470 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7874 (ttmm)
REVERT: A  474 MET cc_start: 0.7611 (mmm) cc_final: 0.7363 (mmm)
REVERT: A  553 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8245 (tptp)
REVERT: A  562 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8604 (ttmt)
REVERT: A  595 LEU cc_start: 0.8520 (mt) cc_final: 0.8181 (mp)
  outliers start: 20
  outliers final: 14
  residues processed: 238
  average time/residue: 0.1882
  time to fit residues: 58.1688
Evaluate side-chains
  247 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 230
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  589 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0970
   chunk 4 optimal weight:    7.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.116851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.097314 restraints weight = 11714.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.87
r_work: 0.3088 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.5986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   6627  Z= 0.206
  Angle     :  0.623  10.676   9008  Z= 0.328
  Chirality :  0.045   0.323    933
  Planarity :  0.004   0.039   1168
  Dihedral  :  5.136  59.290    868
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 28.69 %
    Favored  : 68.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.41 (0.30), residues: 787
  helix:  2.24 (0.27), residues: 390
  sheet:  0.36 (1.01), residues: 27
  loop : -0.45 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 163 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.037   0.002   PHE B 497 
 TYR   0.025   0.002   TYR A 385 
 ARG   0.009   0.001   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06478 (  304)
  hydrogen bonds       : angle       4.60355 (  873)
  metal coordination   : bond        0.00614 (    2)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       1.45704 (    2)
  covalent geometry    : bond        0.00460 ( 6624)
  covalent geometry    : angle       0.62317 ( 9006)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 224
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  338 PHE cc_start: 0.7996 (m-80) cc_final: 0.7549 (m-10)
REVERT: B  400 PHE cc_start: 0.7689 (p90) cc_final: 0.7407 (p90)
REVERT: B  403 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7926 (ttm-80)
REVERT: B  409 GLN cc_start: 0.8257 (mt0) cc_final: 0.8048 (tt0)
REVERT: B  444 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8427 (mtpp)
REVERT: B  462 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8307 (mmmt)
REVERT: B  490 PHE cc_start: 0.8531 (t80) cc_final: 0.8259 (t80)
REVERT: B  509 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7665 (mtt180)
REVERT: A   35 GLU cc_start: 0.8492 (tp30) cc_final: 0.8220 (tp30)
REVERT: A   69 TRP cc_start: 0.8805 (t-100) cc_final: 0.8480 (t-100)
REVERT: A   75 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8416 (tp30)
REVERT: A  126 ILE cc_start: 0.9067 (mt) cc_final: 0.8783 (tt)
REVERT: A  153 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7423 (pp20)
REVERT: A  161 ARG cc_start: 0.8574 (mtt-85) cc_final: 0.8138 (mtt-85)
REVERT: A  166 GLU cc_start: 0.8020 (tp30) cc_final: 0.7544 (tp30)
REVERT: A  188 ASN cc_start: 0.8385 (t0) cc_final: 0.8148 (t0)
REVERT: A  213 ASN cc_start: 0.8465 (m-40) cc_final: 0.8171 (t0)
REVERT: A  225 ASP cc_start: 0.7741 (m-30) cc_final: 0.7470 (m-30)
REVERT: A  312 GLU cc_start: 0.8099 (tt0) cc_final: 0.7780 (tm-30)
REVERT: A  322 ASN cc_start: 0.6390 (p0) cc_final: 0.5902 (p0)
REVERT: A  323 MET cc_start: 0.8263 (mmp) cc_final: 0.8023 (mmm)
REVERT: A  325 GLN cc_start: 0.8176 (mp10) cc_final: 0.7946 (mm-40)
REVERT: A  347 THR cc_start: 0.8460 (m) cc_final: 0.8007 (p)
REVERT: A  360 MET cc_start: 0.8210 (ttp) cc_final: 0.7829 (ttt)
REVERT: A  371 THR cc_start: 0.8538 (m) cc_final: 0.8191 (p)
REVERT: A  436 ILE cc_start: 0.8387 (tp) cc_final: 0.8131 (tt)
REVERT: A  455 MET cc_start: 0.8243 (tmm) cc_final: 0.7998 (tmm)
REVERT: A  462 MET cc_start: 0.8717 (mtt) cc_final: 0.8431 (mtp)
REVERT: A  470 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7999 (ttmm)
REVERT: A  472 GLN cc_start: 0.8111 (mt0) cc_final: 0.7885 (mt0)
REVERT: A  474 MET cc_start: 0.7645 (mmm) cc_final: 0.7382 (mmm)
REVERT: A  516 TYR cc_start: 0.8727 (t80) cc_final: 0.8514 (t80)
REVERT: A  532 ILE cc_start: 0.8833 (mt) cc_final: 0.8613 (tp)
REVERT: A  553 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8328 (mmtt)
  outliers start: 18
  outliers final: 13
  residues processed: 230
  average time/residue: 0.1904
  time to fit residues: 57.2917
Evaluate side-chains
  236 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 221
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain A residue  531 GLN
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  589 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 64 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 ASN
A 586 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.118665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.099185 restraints weight = 11898.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.91
r_work: 0.3127 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.6177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6627  Z= 0.140
  Angle     :  0.580  10.202   9008  Z= 0.306
  Chirality :  0.042   0.253    933
  Planarity :  0.004   0.035   1168
  Dihedral  :  4.976  57.940    868
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 28.26 %
    Favored  : 69.44 %
  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:  1.45 (0.30), residues: 787
  helix:  2.34 (0.27), residues: 386
  sheet:  0.33 (1.02), residues: 27
  loop : -0.48 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 478 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.035   0.001   PHE B 497 
 TYR   0.023   0.001   TYR A 385 
 ARG   0.006   0.000   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05386 (  304)
  hydrogen bonds       : angle       4.46816 (  873)
  metal coordination   : bond        0.00319 (    2)
  SS BOND              : bond        0.00144 (    1)
  SS BOND              : angle       1.47281 (    2)
  covalent geometry    : bond        0.00318 ( 6624)
  covalent geometry    : angle       0.57986 ( 9006)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3349.95 seconds
wall clock time: 58 minutes 32.19 seconds (3512.19 seconds total)