Starting phenix.real_space_refine
on Tue Jul 29 17:49:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t25_40980/07_2025/8t25_40980.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t25_40980/07_2025/8t25_40980.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t25_40980/07_2025/8t25_40980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t25_40980/07_2025/8t25_40980.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t25_40980/07_2025/8t25_40980.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t25_40980/07_2025/8t25_40980.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.041
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 6352 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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4096      2.51       5
     N    1076      2.21       5
     O    1199      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6408
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4895
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 30, 'TRANS': 564}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1513
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 11, 'TRANS': 180}
          Chain breaks: 1
  Time building chain proxies: 6.61, per 1000 atoms: 1.03
  Number of scatterers: 6408
  At special positions: 0
  Unit cell: (101.01, 101.01, 108.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1199      8.00
     N    1076      7.00
     C    4096      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 531 " - pdb=" SG  CYS A 543 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  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: 1.69
  Conformation dependent library (CDL) restraints added in 871.0 milliseconds
  

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1484

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 3 sheets defined
      55.1% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 4.051A  pdb=" N   TYR A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 90 through 102
    Processing helix  chain 'A' and resid 109 through 130
      removed outlier: 4.277A  pdb=" N   SER A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.966A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 219 through 252
      removed outlier: 4.358A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 263 through 267
      removed outlier: 3.964A  pdb=" N   LEU A 267 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 282
      removed outlier: 3.532A  pdb=" N   LEU A 278 " --> pdb=" O   TRP A 275 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR A 279 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
      No H-bonds generated for 'chain 'A' and resid 275 through 282'
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 3.555A  pdb=" N   SER A 301 " --> pdb=" O   MET A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.696A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLY A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.988A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.789A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 466
      removed outlier: 3.727A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      removed outlier: 3.705A  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 519 through 534
      removed outlier: 3.882A  pdb=" N   ILE A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ALA A 534 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 561
      removed outlier: 3.893A  pdb=" N   GLY A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLU A 557 " --> pdb=" O   GLN A 553 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET A 558 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 576
      removed outlier: 3.598A  pdb=" N   GLU A 572 " --> pdb=" O   THR A 568 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG A 573 " --> pdb=" O   PHE A 569 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   VAL A 574 " --> pdb=" O   ALA A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 596
      removed outlier: 3.527A  pdb=" N   LEU A 586 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      Proline residue:  A 591  - end of helix
    Processing helix  chain 'B' and resid 337 through 343
    Processing helix  chain 'B' and resid 385 through 390
      removed outlier: 4.097A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 3.558A  pdb=" N   VAL B 407 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE B 410 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.337A  pdb=" N   ALA A 348 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   LYS A 359 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   ASP A 350 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   ARG A 357 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLY A 352 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 356
      removed outlier: 3.786A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA B 397 " --> pdb=" O   LYS B 356 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR B 396 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER B 514 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL B 512 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU B 513 " --> pdb=" O   CYS B 432 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454

    286 hydrogen bonds defined for protein.
    822 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: 1.60

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2073
        1.35 -     1.47: 1720
        1.47 -     1.59: 2738
        1.59 -     1.71: 1
        1.71 -     1.84: 58
  Bond restraints: 6590
  Sorted by residual:
  bond pdb=" CB  PRO A 346 "
       pdb=" CG  PRO A 346 "
    ideal  model  delta    sigma   weight residual
    1.492  1.606 -0.114 5.00e-02 4.00e+02 5.20e+00
  bond pdb=" CB  PRO A 321 "
       pdb=" CG  PRO A 321 "
    ideal  model  delta    sigma   weight residual
    1.492  1.586 -0.094 5.00e-02 4.00e+02 3.57e+00
  bond pdb=" CA  LYS A 234 "
       pdb=" C   LYS A 234 "
    ideal  model  delta    sigma   weight residual
    1.522  1.540 -0.019 1.29e-02 6.01e+03 2.06e+00
  bond pdb=" CB  LYS A 565 "
       pdb=" CG  LYS A 565 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.28e+00
  bond pdb=" C   LYS A 234 "
       pdb=" N   PRO A 235 "
    ideal  model  delta    sigma   weight residual
    1.335  1.349 -0.014 1.28e-02 6.10e+03 1.28e+00
  ... (remaining 6585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 8719
        1.72 -     3.44: 184
        3.44 -     5.15: 30
        5.15 -     6.87: 11
        6.87 -     8.59: 5
  Bond angle restraints: 8949
  Sorted by residual:
  angle pdb=" CA  PRO A 346 "
        pdb=" N   PRO A 346 "
        pdb=" CD  PRO A 346 "
      ideal   model   delta    sigma   weight residual
     112.00  104.58    7.42 1.40e+00 5.10e-01 2.81e+01
  angle pdb=" CB  LYS A 565 "
        pdb=" CG  LYS A 565 "
        pdb=" CD  LYS A 565 "
      ideal   model   delta    sigma   weight residual
     111.30  119.89   -8.59 2.30e+00 1.89e-01 1.39e+01
  angle pdb=" CA  PRO A 321 "
        pdb=" N   PRO A 321 "
        pdb=" CD  PRO A 321 "
      ideal   model   delta    sigma   weight residual
     112.00  107.10    4.90 1.40e+00 5.10e-01 1.22e+01
  angle pdb=" CA  LYS A 470 "
        pdb=" CB  LYS A 470 "
        pdb=" CG  LYS A 470 "
      ideal   model   delta    sigma   weight residual
     114.10  120.28   -6.18 2.00e+00 2.50e-01 9.54e+00
  angle pdb=" N   LEU A 450 "
        pdb=" CA  LEU A 450 "
        pdb=" C   LEU A 450 "
      ideal   model   delta    sigma   weight residual
     109.81  116.62   -6.81 2.21e+00 2.05e-01 9.50e+00
  ... (remaining 8944 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 3268
       17.54 -    35.08: 455
       35.08 -    52.62: 146
       52.62 -    70.16: 17
       70.16 -    87.70: 13
  Dihedral angle restraints: 3899
    sinusoidal: 1590
      harmonic: 2309
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.44   46.56     1      1.00e+01 1.00e-02 3.00e+01
  dihedral pdb=" CA  CYS B 379 "
           pdb=" C   CYS B 379 "
           pdb=" N   TYR B 380 "
           pdb=" CA  TYR B 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.45  -21.55     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.67  -34.67     1      1.00e+01 1.00e-02 1.70e+01
  ... (remaining 3896 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 784
       0.054 -    0.109: 119
       0.109 -    0.163: 20
       0.163 -    0.217: 0
       0.217 -    0.272: 1
  Chirality restraints: 924
  Sorted by residual:
  chirality pdb=" CB  VAL A 582 "
            pdb=" CA  VAL A 582 "
            pdb=" CG1 VAL A 582 "
            pdb=" CG2 VAL A 582 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CB  THR A 371 "
            pdb=" CA  THR A 371 "
            pdb=" OG1 THR A 371 "
            pdb=" CG2 THR A 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  LYS A 234 "
            pdb=" N   LYS A 234 "
            pdb=" C   LYS A 234 "
            pdb=" CB  LYS A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 921 not shown)

  Planarity restraints: 1164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 345 "    0.079 5.00e-02 4.00e+02   1.15e-01 2.12e+01
        pdb=" N   PRO A 346 "   -0.199 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  90 "   -0.065 5.00e-02 4.00e+02   9.67e-02 1.50e+01
        pdb=" N   PRO A  91 "    0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO A  91 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A  91 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 320 "   -0.035 5.00e-02 4.00e+02   5.17e-02 4.27e+00
        pdb=" N   PRO A 321 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1161 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 527
        2.74 -     3.28: 6393
        3.28 -     3.82: 10584
        3.82 -     4.36: 11280
        4.36 -     4.90: 19478
  Nonbonded interactions: 48262
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OG1 THR B 500 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG1 THR A 365 "
            pdb=" OD1 ASP A 368 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OD2 ASP A 435 "
            pdb=" OH  TYR A 541 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   SER A 155 "
            pdb=" NH1 ARG A 161 "
     model   vdw
     2.310 3.120
  ... (remaining 48257 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.010
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5926
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.114   6596  Z= 0.136
  Angle     :  0.628   8.588   8961  Z= 0.330
  Chirality :  0.041   0.272    924
  Planarity :  0.006   0.115   1164
  Dihedral  : 18.086  87.703   2397
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 29.51 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.29), residues: 777
  helix:  1.20 (0.27), residues: 365
  sheet:  0.41 (1.17), residues: 24
  loop : -1.64 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  69 
 HIS   0.006   0.001   HIS A 417 
 PHE   0.010   0.001   PHE B 338 
 TYR   0.015   0.001   TYR B 508 
 ARG   0.002   0.000   ARG A 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11418 (  286)
  hydrogen bonds       : angle       4.62424 (  822)
  SS BOND              : bond        0.00802 (    6)
  SS BOND              : angle       1.14799 (   12)
  covalent geometry    : bond        0.00333 ( 6590)
  covalent geometry    : angle       0.62740 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.735 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1908
  time to fit residues: 19.9525
Evaluate side-chains
  74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0010
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0570
   chunk 45 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.4704

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
A 523 GLN
** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.192422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.173764 restraints weight = 12076.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.176081 restraints weight = 8626.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.177661 restraints weight = 6644.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6077
moved from start:          0.0767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6596  Z= 0.129
  Angle     :  0.574  10.085   8961  Z= 0.289
  Chirality :  0.041   0.169    924
  Planarity :  0.005   0.068   1164
  Dihedral  :  4.156  21.761    861
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.42 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.29), residues: 777
  helix:  1.32 (0.27), residues: 365
  sheet: -0.86 (1.01), residues: 27
  loop : -1.55 (0.28), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  69 
 HIS   0.006   0.001   HIS A 417 
 PHE   0.016   0.001   PHE B 338 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.004   0.001   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05395 (  286)
  hydrogen bonds       : angle       4.37965 (  822)
  SS BOND              : bond        0.00659 (    6)
  SS BOND              : angle       1.13512 (   12)
  covalent geometry    : bond        0.00281 ( 6590)
  covalent geometry    : angle       0.57326 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 76
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  512 PHE cc_start: 0.4593 (OUTLIER) cc_final: 0.4243 (t80)
REVERT: B  406 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6964 (mm-30)
  outliers start: 31
  outliers final: 16
  residues processed: 98
  average time/residue: 0.1472
  time to fit residues: 20.5773
Evaluate side-chains
  88 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  523 GLN
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0970
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.188768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.169915 restraints weight = 12126.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.171949 restraints weight = 8663.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.173696 restraints weight = 6765.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6178
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6596  Z= 0.154
  Angle     :  0.604   9.250   8961  Z= 0.305
  Chirality :  0.043   0.214    924
  Planarity :  0.005   0.059   1164
  Dihedral  :  4.373  23.164    861
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 24.42 %
    Favored  : 69.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.29), residues: 777
  helix:  1.39 (0.28), residues: 359
  sheet: -1.22 (0.99), residues: 27
  loop : -1.67 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 417 
 PHE   0.011   0.001   PHE B 400 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06287 (  286)
  hydrogen bonds       : angle       4.45905 (  822)
  SS BOND              : bond        0.00639 (    6)
  SS BOND              : angle       1.32762 (   12)
  covalent geometry    : bond        0.00335 ( 6590)
  covalent geometry    : angle       0.60228 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 79
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A  169 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6481 (ttm170)
REVERT: A  203 TRP cc_start: 0.5845 (OUTLIER) cc_final: 0.5104 (m-10)
REVERT: A  438 PHE cc_start: 0.5408 (OUTLIER) cc_final: 0.4729 (t80)
REVERT: A  512 PHE cc_start: 0.4906 (OUTLIER) cc_final: 0.4396 (t80)
  outliers start: 39
  outliers final: 24
  residues processed: 111
  average time/residue: 0.1742
  time to fit residues: 26.3745
Evaluate side-chains
  99 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  587 ASN
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 73 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 523 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.187398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.170034 restraints weight = 12358.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.170892 restraints weight = 9511.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.172848 restraints weight = 8208.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6207
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6596  Z= 0.159
  Angle     :  0.617   9.721   8961  Z= 0.313
  Chirality :  0.043   0.230    924
  Planarity :  0.005   0.053   1164
  Dihedral  :  4.540  23.852    861
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  6.98 %
    Allowed  : 24.27 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.29), residues: 777
  helix:  1.18 (0.27), residues: 368
  sheet: -1.39 (0.98), residues: 27
  loop : -1.80 (0.28), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 417 
 PHE   0.011   0.001   PHE B 400 
 TYR   0.018   0.002   TYR A 202 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06590 (  286)
  hydrogen bonds       : angle       4.52902 (  822)
  SS BOND              : bond        0.00638 (    6)
  SS BOND              : angle       1.43215 (   12)
  covalent geometry    : bond        0.00346 ( 6590)
  covalent geometry    : angle       0.61488 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 75
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 THR cc_start: -0.1212 (OUTLIER) cc_final: -0.1645 (p)
REVERT: A  169 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6225 (ttm170)
REVERT: A  203 TRP cc_start: 0.5716 (OUTLIER) cc_final: 0.4948 (m-10)
REVERT: A  438 PHE cc_start: 0.5384 (OUTLIER) cc_final: 0.4702 (t80)
REVERT: A  512 PHE cc_start: 0.5049 (OUTLIER) cc_final: 0.4483 (t80)
  outliers start: 48
  outliers final: 30
  residues processed: 115
  average time/residue: 0.1609
  time to fit residues: 25.6155
Evaluate side-chains
  103 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 68
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  587 ASN
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  365 TYR
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  424 LYS
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0570
   chunk 65 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6500

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.187697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.169985 restraints weight = 12280.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.171680 restraints weight = 9697.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.173343 restraints weight = 7890.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6196
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6596  Z= 0.147
  Angle     :  0.608   9.832   8961  Z= 0.307
  Chirality :  0.043   0.231    924
  Planarity :  0.004   0.050   1164
  Dihedral  :  4.510  23.966    861
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 24.85 %
    Favored  : 69.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.29), residues: 777
  helix:  1.22 (0.27), residues: 363
  sheet: -1.63 (0.87), residues: 32
  loop : -1.81 (0.28), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  69 
 HIS   0.007   0.001   HIS A 417 
 PHE   0.009   0.001   PHE B 400 
 TYR   0.016   0.001   TYR A 202 
 ARG   0.003   0.000   ARG A 519 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06323 (  286)
  hydrogen bonds       : angle       4.51571 (  822)
  SS BOND              : bond        0.00904 (    6)
  SS BOND              : angle       1.43648 (   12)
  covalent geometry    : bond        0.00316 ( 6590)
  covalent geometry    : angle       0.60638 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 74
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 THR cc_start: -0.1268 (OUTLIER) cc_final: -0.1703 (p)
REVERT: A  169 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6268 (ttm170)
REVERT: A  203 TRP cc_start: 0.5766 (OUTLIER) cc_final: 0.4994 (m-10)
REVERT: A  438 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.4688 (t80)
REVERT: A  512 PHE cc_start: 0.4868 (OUTLIER) cc_final: 0.4285 (t80)
REVERT: A  558 MET cc_start: 0.6974 (tpt) cc_final: 0.6603 (mmm)
  outliers start: 42
  outliers final: 29
  residues processed: 109
  average time/residue: 0.1608
  time to fit residues: 24.0059
Evaluate side-chains
  106 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 72
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  587 ASN
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  365 TYR
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  424 LYS
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0470
   chunk 37 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0870
   chunk 12 optimal weight:    0.0670
   chunk 35 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.2594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.191437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.173047 restraints weight = 12045.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.175582 restraints weight = 8512.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.176891 restraints weight = 6466.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6096
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6596  Z= 0.123
  Angle     :  0.573  10.446   8961  Z= 0.288
  Chirality :  0.041   0.253    924
  Planarity :  0.004   0.050   1164
  Dihedral  :  4.269  23.084    861
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 26.45 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.29), residues: 777
  helix:  1.38 (0.27), residues: 365
  sheet: -1.60 (0.85), residues: 32
  loop : -1.67 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  69 
 HIS   0.010   0.001   HIS A 417 
 PHE   0.008   0.001   PHE A 438 
 TYR   0.023   0.001   TYR A 202 
 ARG   0.006   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05254 (  286)
  hydrogen bonds       : angle       4.41695 (  822)
  SS BOND              : bond        0.00573 (    6)
  SS BOND              : angle       1.28171 (   12)
  covalent geometry    : bond        0.00255 ( 6590)
  covalent geometry    : angle       0.57165 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6173 (ttm170)
REVERT: A  438 PHE cc_start: 0.5387 (OUTLIER) cc_final: 0.4908 (t80)
REVERT: A  512 PHE cc_start: 0.4834 (OUTLIER) cc_final: 0.4337 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 101
  average time/residue: 0.1838
  time to fit residues: 25.4995
Evaluate side-chains
  94 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  424 LYS
Chi-restraints excluded: chain B residue  490 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0980
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
B 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.187103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.168142 restraints weight = 11853.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.170186 restraints weight = 8017.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.172322 restraints weight = 6233.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6596  Z= 0.156
  Angle     :  0.616   9.947   8961  Z= 0.313
  Chirality :  0.043   0.254    924
  Planarity :  0.005   0.045   1164
  Dihedral  :  4.520  25.216    861
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 26.16 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.29), residues: 777
  helix:  1.30 (0.27), residues: 358
  sheet: -1.41 (0.97), residues: 27
  loop : -1.74 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  69 
 HIS   0.007   0.001   HIS A 417 
 PHE   0.011   0.001   PHE B 429 
 TYR   0.016   0.001   TYR B 351 
 ARG   0.006   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06406 (  286)
  hydrogen bonds       : angle       4.47794 (  822)
  SS BOND              : bond        0.00778 (    6)
  SS BOND              : angle       1.43930 (   12)
  covalent geometry    : bond        0.00342 ( 6590)
  covalent geometry    : angle       0.61463 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 78
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 THR cc_start: -0.1330 (OUTLIER) cc_final: -0.1768 (p)
REVERT: A  169 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6146 (ttm170)
REVERT: A  438 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.4425 (t80)
REVERT: A  512 PHE cc_start: 0.5053 (OUTLIER) cc_final: 0.4393 (t80)
  outliers start: 39
  outliers final: 25
  residues processed: 113
  average time/residue: 0.1617
  time to fit residues: 25.0893
Evaluate side-chains
  104 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  424 LYS
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0770
   chunk 43 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 50 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
B 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.188418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.170064 restraints weight = 12112.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.171977 restraints weight = 8608.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.173290 restraints weight = 7554.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6184
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6596  Z= 0.143
  Angle     :  0.612  11.024   8961  Z= 0.311
  Chirality :  0.043   0.285    924
  Planarity :  0.004   0.045   1164
  Dihedral  :  4.515  25.371    861
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 27.47 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.29), residues: 777
  helix:  1.24 (0.27), residues: 359
  sheet: -1.67 (0.87), residues: 32
  loop : -1.74 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  69 
 HIS   0.007   0.001   HIS A 417 
 PHE   0.010   0.001   PHE B 377 
 TYR   0.015   0.001   TYR A 202 
 ARG   0.003   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06055 (  286)
  hydrogen bonds       : angle       4.49588 (  822)
  SS BOND              : bond        0.00669 (    6)
  SS BOND              : angle       1.45168 (   12)
  covalent geometry    : bond        0.00314 ( 6590)
  covalent geometry    : angle       0.61052 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 74
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 THR cc_start: -0.1390 (OUTLIER) cc_final: -0.1823 (p)
REVERT: A  169 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6116 (ttm170)
REVERT: A  438 PHE cc_start: 0.5465 (OUTLIER) cc_final: 0.4404 (t80)
REVERT: A  512 PHE cc_start: 0.4962 (OUTLIER) cc_final: 0.4377 (t80)
  outliers start: 34
  outliers final: 27
  residues processed: 101
  average time/residue: 0.1846
  time to fit residues: 25.0284
Evaluate side-chains
  105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  365 TYR
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  424 LYS
Chi-restraints excluded: chain B residue  501 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 58 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
B 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.187098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.168355 restraints weight = 12246.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.170354 restraints weight = 8839.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.171520 restraints weight = 7835.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6227
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6596  Z= 0.156
  Angle     :  0.635  10.760   8961  Z= 0.322
  Chirality :  0.044   0.290    924
  Planarity :  0.005   0.044   1164
  Dihedral  :  4.603  26.787    861
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 26.31 %
    Favored  : 67.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.29), residues: 777
  helix:  1.20 (0.27), residues: 358
  sheet: -1.80 (0.86), residues: 32
  loop : -1.79 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  69 
 HIS   0.003   0.001   HIS A 265 
 PHE   0.011   0.001   PHE B 377 
 TYR   0.014   0.001   TYR A 202 
 ARG   0.004   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06389 (  286)
  hydrogen bonds       : angle       4.51975 (  822)
  SS BOND              : bond        0.00775 (    6)
  SS BOND              : angle       1.48168 (   12)
  covalent geometry    : bond        0.00345 ( 6590)
  covalent geometry    : angle       0.63316 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 74
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 THR cc_start: -0.1357 (OUTLIER) cc_final: -0.1789 (p)
REVERT: A  169 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6023 (ttm170)
REVERT: A  438 PHE cc_start: 0.5408 (OUTLIER) cc_final: 0.4462 (t80)
REVERT: A  512 PHE cc_start: 0.4970 (OUTLIER) cc_final: 0.4317 (t80)
  outliers start: 41
  outliers final: 31
  residues processed: 108
  average time/residue: 0.1781
  time to fit residues: 26.4850
Evaluate side-chains
  110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 75
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  365 TYR
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  424 LYS
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  501 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.0670
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 68 optimal weight:    0.1980
   chunk 54 optimal weight:    0.8980
   chunk 51 optimal weight:    0.2980
   chunk 76 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
B 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.189580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.171133 restraints weight = 12272.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.172703 restraints weight = 8695.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.174068 restraints weight = 7903.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6175
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6596  Z= 0.135
  Angle     :  0.612  11.233   8961  Z= 0.308
  Chirality :  0.043   0.295    924
  Planarity :  0.004   0.044   1164
  Dihedral  :  4.502  26.696    861
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 27.03 %
    Favored  : 67.88 %
  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: -0.43 (0.29), residues: 777
  helix:  1.26 (0.27), residues: 359
  sheet: -1.75 (0.87), residues: 32
  loop : -1.73 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  69 
 HIS   0.002   0.001   HIS A 417 
 PHE   0.009   0.001   PHE B 377 
 TYR   0.015   0.001   TYR A 202 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05806 (  286)
  hydrogen bonds       : angle       4.47040 (  822)
  SS BOND              : bond        0.00700 (    6)
  SS BOND              : angle       1.45124 (   12)
  covalent geometry    : bond        0.00293 ( 6590)
  covalent geometry    : angle       0.60996 ( 8949)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 73
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 THR cc_start: -0.1402 (OUTLIER) cc_final: -0.1837 (p)
REVERT: A  169 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6087 (ttm170)
REVERT: A  438 PHE cc_start: 0.5460 (OUTLIER) cc_final: 0.4736 (t80)
REVERT: A  512 PHE cc_start: 0.4765 (OUTLIER) cc_final: 0.4127 (t80)
  outliers start: 35
  outliers final: 27
  residues processed: 100
  average time/residue: 0.2110
  time to fit residues: 28.6304
Evaluate side-chains
  104 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 73
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  365 TYR
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  424 LYS
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  501 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0170
   chunk 21 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0070
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.2836

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
B 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.190576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.171894 restraints weight = 12379.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.173400 restraints weight = 8689.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.175455 restraints weight = 7142.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6123
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6596  Z= 0.128
  Angle     :  0.596  11.162   8961  Z= 0.300
  Chirality :  0.042   0.282    924
  Planarity :  0.004   0.043   1164
  Dihedral  :  4.364  26.248    861
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 27.33 %
    Favored  : 67.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.29), residues: 777
  helix:  1.35 (0.27), residues: 359
  sheet: -1.73 (0.86), residues: 32
  loop : -1.69 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  69 
 HIS   0.002   0.001   HIS A 417 
 PHE   0.009   0.001   PHE B 377 
 TYR   0.017   0.001   TYR A 202 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05384 (  286)
  hydrogen bonds       : angle       4.43796 (  822)
  SS BOND              : bond        0.00671 (    6)
  SS BOND              : angle       1.37163 (   12)
  covalent geometry    : bond        0.00275 ( 6590)
  covalent geometry    : angle       0.59391 ( 8949)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4324.97 seconds
wall clock time: 78 minutes 31.84 seconds (4711.84 seconds total)