Starting phenix.real_space_refine
on Wed Sep 17 05:50:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l7q_23216/09_2025/7l7q_23216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l7q_23216/09_2025/7l7q_23216.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l7q_23216/09_2025/7l7q_23216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l7q_23216/09_2025/7l7q_23216.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l7q_23216/09_2025/7l7q_23216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l7q_23216/09_2025/7l7q_23216.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    3599      2.51       5
     N     951      2.21       5
     O    1042      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5619
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 1113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1113
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 1, 'TRANS': 131}
    Chain: "I"
      Number of atoms: 3480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3480
          Classifications: {'peptide': 427}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 411}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
    Chain: "K"
      Number of atoms: 1026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1026
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
  Time building chain proxies: 1.45, per 1000 atoms: 0.26
  Number of scatterers: 5619
  At special positions: 0
  Unit cell: (103.125, 87.45, 88.275, 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      27     16.00
     O    1042      8.00
     N     951      7.00
     C    3599      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 215.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      72.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'H' and resid 3 through 39
      removed outlier: 4.119A  pdb=" N   LEU H  35 " --> pdb=" O   ASP H  31 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 46 through 72
      removed outlier: 3.616A  pdb=" N   LEU H  53 " --> pdb=" O   GLN H  49 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU H  68 " --> pdb=" O   GLU H  64 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU H  69 " --> pdb=" O   LYS H  65 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 89
      removed outlier: 3.580A  pdb=" N   GLN H  87 " --> pdb=" O   PHE H  83 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASN H  88 " --> pdb=" O   THR H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 96
      removed outlier: 4.369A  pdb=" N   ASN H  94 " --> pdb=" O   LEU H  90 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER H  95 " --> pdb=" O   GLU H  91 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   LEU H  96 " --> pdb=" O   GLU H  92 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 90 through 96'
    Processing helix  chain 'H' and resid 96 through 109
      removed outlier: 3.513A  pdb=" N   LEU H 100 " --> pdb=" O   LEU H  96 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU H 101 " --> pdb=" O   ASP H  97 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLN H 107 " --> pdb=" O   SER H 103 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 109 through 134
      removed outlier: 3.847A  pdb=" N   LYS H 127 " --> pdb=" O   GLU H 123 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 295 through 302
    Processing helix  chain 'I' and resid 311 through 317
      removed outlier: 3.536A  pdb=" N   LYS I 317 " --> pdb=" O   ASP I 313 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 336 through 348
      removed outlier: 4.241A  pdb=" N   SER I 341 " --> pdb=" O   LYS I 337 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   SER I 342 " --> pdb=" O   HIS I 338 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU I 345 " --> pdb=" O   SER I 341 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE I 346 " --> pdb=" O   SER I 342 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ASN I 348 " --> pdb=" O   ILE I 344 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 354 through 369
    Processing helix  chain 'I' and resid 374 through 388
      removed outlier: 4.135A  pdb=" N   VAL I 378 " --> pdb=" O   THR I 374 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE I 379 " --> pdb=" O   PRO I 375 " (cutoff:3.500A)
      Proline residue:  I 380  - end of helix
      removed outlier: 3.576A  pdb=" N   MET I 388 " --> pdb=" O   SER I 384 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 389 through 401
      removed outlier: 3.637A  pdb=" N   ARG I 395 " --> pdb=" O   LYS I 391 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 409 through 421
      removed outlier: 3.674A  pdb=" N   LEU I 413 " --> pdb=" O   ASP I 409 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS I 414 " --> pdb=" O   GLU I 410 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 429 through 431
      No H-bonds generated for 'chain 'I' and resid 429 through 431'
    Processing helix  chain 'I' and resid 432 through 448
    Processing helix  chain 'I' and resid 456 through 475
      removed outlier: 3.712A  pdb=" N   THR I 461 " --> pdb=" O   THR I 457 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASP I 475 " --> pdb=" O   ASN I 471 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 478 through 494
      removed outlier: 4.654A  pdb=" N   HIS I 487 " --> pdb=" O   LEU I 483 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASP I 488 " --> pdb=" O   THR I 484 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 506 through 525
      removed outlier: 3.738A  pdb=" N   SER I 514 " --> pdb=" O   MET I 510 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU I 519 " --> pdb=" O   SER I 515 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 531 through 535
    Processing helix  chain 'I' and resid 538 through 547
      removed outlier: 4.872A  pdb=" N   LYS I 544 " --> pdb=" O   ASP I 540 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL I 545 " --> pdb=" O   ILE I 541 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 550 through 563
    Processing helix  chain 'I' and resid 564 through 568
    Processing helix  chain 'I' and resid 577 through 589
      removed outlier: 3.571A  pdb=" N   GLN I 583 " --> pdb=" O   ARG I 579 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 608 through 616
      removed outlier: 3.526A  pdb=" N   LYS I 612 " --> pdb=" O   PRO I 608 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 640 through 654
      removed outlier: 3.648A  pdb=" N   GLU I 654 " --> pdb=" O   LEU I 650 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 666 through 676
      removed outlier: 3.784A  pdb=" N   ASN I 671 " --> pdb=" O   GLU I 667 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE I 673 " --> pdb=" O   THR I 669 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 677 through 684
      removed outlier: 3.565A  pdb=" N   ILE I 681 " --> pdb=" O   HIS I 677 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 692 through 705
    Processing helix  chain 'I' and resid 709 through 711
      No H-bonds generated for 'chain 'I' and resid 709 through 711'
    Processing helix  chain 'I' and resid 712 through 723
      removed outlier: 3.554A  pdb=" N   ALA I 716 " --> pdb=" O   ARG I 712 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   LYS I 723 " --> pdb=" O   PHE I 719 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 6 through 40
    Processing helix  chain 'K' and resid 69 through 129
      removed outlier: 4.354A  pdb=" N   PHE K  78 " --> pdb=" O   LEU K  74 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER K  80 " --> pdb=" O   SER K  76 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER K  86 " --> pdb=" O   ARG K  82 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   SER K  87 " --> pdb=" O   ALA K  83 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   GLU K  88 " --> pdb=" O   GLN K  84 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASP K  99 " --> pdb=" O   ASP K  95 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG K 119 " --> pdb=" O   LYS K 115 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    951 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.85

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1790
        1.34 -     1.45: 838
        1.45 -     1.57: 3051
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 5725
  Sorted by residual:
  bond pdb=" C   ASP K  68 "
       pdb=" N   PRO K  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.317  0.016 8.40e-03 1.42e+04 3.76e+00
  bond pdb=" CA  GLU I 616 "
       pdb=" CB  GLU I 616 "
    ideal  model  delta    sigma   weight residual
    1.529  1.503  0.026 1.66e-02 3.63e+03 2.44e+00
  bond pdb=" N   THR I 634 "
       pdb=" CA  THR I 634 "
    ideal  model  delta    sigma   weight residual
    1.464  1.443  0.020 1.30e-02 5.92e+03 2.44e+00
  bond pdb=" CB  CYS I 643 "
       pdb=" SG  CYS I 643 "
    ideal  model  delta    sigma   weight residual
    1.808  1.758  0.050 3.30e-02 9.18e+02 2.29e+00
  bond pdb=" CA  PRO K  60 "
       pdb=" C   PRO K  60 "
    ideal  model  delta    sigma   weight residual
    1.525  1.512  0.014 9.70e-03 1.06e+04 2.04e+00
  ... (remaining 5720 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 7565
        2.52 -     5.05: 144
        5.05 -     7.57: 17
        7.57 -    10.09: 1
       10.09 -    12.62: 1
  Bond angle restraints: 7728
  Sorted by residual:
  angle pdb=" C   ASP I 549 "
        pdb=" N   ASP I 550 "
        pdb=" CA  ASP I 550 "
      ideal   model   delta    sigma   weight residual
     120.67  108.05   12.62 1.34e+00 5.57e-01 8.87e+01
  angle pdb=" N   ALA I 708 "
        pdb=" CA  ALA I 708 "
        pdb=" C   ALA I 708 "
      ideal   model   delta    sigma   weight residual
     114.75  106.21    8.54 1.26e+00 6.30e-01 4.59e+01
  angle pdb=" N   PRO I 318 "
        pdb=" CA  PRO I 318 "
        pdb=" CB  PRO I 318 "
      ideal   model   delta    sigma   weight residual
     103.00  110.31   -7.31 1.10e+00 8.26e-01 4.42e+01
  angle pdb=" N   THR I 564 "
        pdb=" CA  THR I 564 "
        pdb=" C   THR I 564 "
      ideal   model   delta    sigma   weight residual
     114.75  107.82    6.93 1.26e+00 6.30e-01 3.03e+01
  angle pdb=" N   GLY I 605 "
        pdb=" CA  GLY I 605 "
        pdb=" C   GLY I 605 "
      ideal   model   delta    sigma   weight residual
     114.69  109.20    5.49 1.19e+00 7.06e-01 2.13e+01
  ... (remaining 7723 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 3063
       17.58 -    35.16: 349
       35.16 -    52.74: 70
       52.74 -    70.32: 8
       70.32 -    87.90: 9
  Dihedral angle restraints: 3499
    sinusoidal: 1454
      harmonic: 2045
  Sorted by residual:
  dihedral pdb=" CA  GLY I 663 "
           pdb=" C   GLY I 663 "
           pdb=" N   ILE I 664 "
           pdb=" CA  ILE I 664 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.95   31.05     0      5.00e+00 4.00e-02 3.86e+01
  dihedral pdb=" CA  SER I 662 "
           pdb=" C   SER I 662 "
           pdb=" N   GLY I 663 "
           pdb=" CA  GLY I 663 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  PHE I 368 "
           pdb=" C   PHE I 368 "
           pdb=" N   ALA I 369 "
           pdb=" CA  ALA I 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.19   20.81     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 3496 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 659
       0.049 -    0.098: 203
       0.098 -    0.146: 20
       0.146 -    0.195: 2
       0.195 -    0.244: 2
  Chirality restraints: 886
  Sorted by residual:
  chirality pdb=" CA  PRO I 318 "
            pdb=" N   PRO I 318 "
            pdb=" C   PRO I 318 "
            pdb=" CB  PRO I 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CB  ILE I 665 "
            pdb=" CA  ILE I 665 "
            pdb=" CG1 ILE I 665 "
            pdb=" CG2 ILE I 665 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ILE I 633 "
            pdb=" N   ILE I 633 "
            pdb=" C   ILE I 633 "
            pdb=" CB  ILE I 633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.02e-01
  ... (remaining 883 not shown)

  Planarity restraints: 969
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP H  97 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.75e+00
        pdb=" C   ASP H  97 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP H  97 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR H  98 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY I 538 "    0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO I 539 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO I 539 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO I 539 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU I 421 "   -0.018 5.00e-02 4.00e+02   2.73e-02 1.19e+00
        pdb=" N   PRO I 422 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO I 422 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO I 422 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 966 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 64
        2.48 -     3.08: 4601
        3.08 -     3.69: 9262
        3.69 -     4.29: 12897
        4.29 -     4.90: 19936
  Nonbonded interactions: 46760
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU H  99 "
            pdb=" CD2 LEU K  90 "
     model   vdw
     1.873 3.460
  nonbonded pdb=" O   ILE I 382 "
            pdb=" OG  SER I 386 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" CE1 TYR H  98 "
            pdb=" O   ALA I 708 "
     model   vdw
     2.140 3.340
  nonbonded pdb=" O   PHE I 512 "
            pdb=" OG  SER I 515 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" O   PHE I 439 "
            pdb=" OG  SER I 442 "
     model   vdw
     2.200 3.040
  ... (remaining 46755 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:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.890
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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      :  0.005   0.050   5725  Z= 0.278
  Angle     :  0.911  12.619   7728  Z= 0.600
  Chirality :  0.045   0.244    886
  Planarity :  0.004   0.034    969
  Dihedral  : 15.540  87.901   2159
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 23.76
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 10.16 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  8.40 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.40 (0.25), residues: 679
  helix: -2.55 (0.18), residues: 450
  sheet:  None (None), residues: 0
  loop : -3.38 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  24 
 TYR   0.015   0.002   TYR I 641 
 PHE   0.013   0.002   PHE H 135 
 TRP   0.013   0.002   TRP I 446 
 HIS   0.006   0.002   HIS I 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 5725)
  covalent geometry    : angle       0.91064 ( 7728)
  hydrogen bonds       : bond        0.19695 (  321)
  hydrogen bonds       : angle       7.42722 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    7 LYS cc_start: 0.9341 (tmmt) cc_final: 0.9104 (pttp)
REVERT: H   50 GLN cc_start: 0.8838 (tp40) cc_final: 0.8273 (tm-30)
REVERT: H   54 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8392 (mt-10)
REVERT: H   71 ARG cc_start: 0.8604 (ptp90) cc_final: 0.8369 (ptp-110)
REVERT: H  118 ARG cc_start: 0.8822 (ttt90) cc_final: 0.8236 (tmm160)
REVERT: H  122 ASP cc_start: 0.8832 (t0) cc_final: 0.8618 (t0)
REVERT: I  337 LYS cc_start: 0.8869 (tttt) cc_final: 0.7983 (tttt)
REVERT: I  340 TYR cc_start: 0.8532 (m-10) cc_final: 0.8213 (m-10)
REVERT: I  362 TRP cc_start: 0.8785 (t60) cc_final: 0.8292 (t60)
REVERT: I  404 LYS cc_start: 0.9754 (tptp) cc_final: 0.9470 (tptp)
REVERT: I  413 LEU cc_start: 0.9266 (tp) cc_final: 0.8939 (tt)
REVERT: I  417 CYS cc_start: 0.9024 (m) cc_final: 0.8584 (m)
REVERT: I  510 MET cc_start: 0.9214 (tpt) cc_final: 0.8935 (tpp)
REVERT: I  530 TYR cc_start: 0.6931 (p90) cc_final: 0.6464 (p90)
REVERT: I  549 ASP cc_start: 0.7439 (t70) cc_final: 0.7093 (t0)
REVERT: I  586 MET cc_start: 0.7739 (tmm) cc_final: 0.7391 (tmm)
REVERT: I  592 LEU cc_start: 0.8996 (mt) cc_final: 0.8785 (mt)
REVERT: I  664 ILE cc_start: 0.8595 (mm) cc_final: 0.8197 (mm)
REVERT: I  721 TYR cc_start: 0.7910 (m-80) cc_final: 0.7556 (m-80)
REVERT: K   12 ILE cc_start: 0.9257 (mt) cc_final: 0.8837 (mt)
REVERT: K   16 GLU cc_start: 0.9304 (tp30) cc_final: 0.8927 (mt-10)
REVERT: K   46 LYS cc_start: 0.9244 (mmmt) cc_final: 0.8828 (mmmm)
REVERT: K   88 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8443 (mp0)
REVERT: K  113 ASP cc_start: 0.8814 (m-30) cc_final: 0.8610 (m-30)
REVERT: K  116 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8423 (tm-30)
REVERT: K  123 HIS cc_start: 0.9024 (t-90) cc_final: 0.8580 (t70)
REVERT: K  127 ILE cc_start: 0.9219 (tp) cc_final: 0.8848 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1121
  time to fit residues: 23.3915
Evaluate side-chains
  123 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** H   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  19 HIS
H  41 HIS
I 363 GLN
I 390 ASN
I 525 GLN
I 684 HIS
I 703 HIS
K  18 GLN
K 100 GLN
K 111 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.073794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.061128 restraints weight = 23525.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.063249 restraints weight = 13177.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.064746 restraints weight = 8825.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.065806 restraints weight = 6553.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.066560 restraints weight = 5238.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5725  Z= 0.160
  Angle     :  0.745   9.009   7728  Z= 0.389
  Chirality :  0.045   0.336    886
  Planarity :  0.004   0.034    969
  Dihedral  :  5.756  26.879    735
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.81 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 15.86 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (0.31), residues: 679
  helix: -0.60 (0.23), residues: 465
  sheet:  None (None), residues: 0
  loop : -2.76 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K 119 
 TYR   0.014   0.002   TYR I 584 
 PHE   0.017   0.001   PHE I 546 
 TRP   0.010   0.001   TRP K  89 
 HIS   0.004   0.001   HIS I 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5725)
  covalent geometry    : angle       0.74461 ( 7728)
  hydrogen bonds       : bond        0.04975 (  321)
  hydrogen bonds       : angle       4.82049 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   50 GLN cc_start: 0.8723 (tp40) cc_final: 0.8257 (tm-30)
REVERT: H   54 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8465 (mt-10)
REVERT: H   62 ASN cc_start: 0.8961 (t0) cc_final: 0.8397 (t0)
REVERT: H   64 GLU cc_start: 0.8710 (tt0) cc_final: 0.8502 (tt0)
REVERT: H   97 ASP cc_start: 0.8278 (m-30) cc_final: 0.7690 (m-30)
REVERT: H  118 ARG cc_start: 0.8739 (ttt90) cc_final: 0.8030 (tmm160)
REVERT: H  122 ASP cc_start: 0.8873 (t0) cc_final: 0.8627 (t0)
REVERT: I  337 LYS cc_start: 0.8842 (tttt) cc_final: 0.8008 (tptt)
REVERT: I  352 GLU cc_start: 0.9238 (mp0) cc_final: 0.8798 (mm-30)
REVERT: I  358 GLU cc_start: 0.8265 (mp0) cc_final: 0.7962 (mp0)
REVERT: I  362 TRP cc_start: 0.8789 (t60) cc_final: 0.7400 (t60)
REVERT: I  366 ARG cc_start: 0.9145 (ptm160) cc_final: 0.8079 (ptm160)
REVERT: I  388 MET cc_start: 0.8465 (mtt) cc_final: 0.8160 (mmt)
REVERT: I  390 ASN cc_start: 0.6723 (OUTLIER) cc_final: 0.6501 (t0)
REVERT: I  413 LEU cc_start: 0.9235 (tp) cc_final: 0.8993 (tt)
REVERT: I  417 CYS cc_start: 0.8969 (m) cc_final: 0.8497 (m)
REVERT: I  498 ILE cc_start: 0.9277 (tt) cc_final: 0.9007 (pt)
REVERT: I  565 LYS cc_start: 0.8636 (tmtt) cc_final: 0.7717 (tppt)
REVERT: I  586 MET cc_start: 0.7921 (tmm) cc_final: 0.7546 (tmm)
REVERT: I  631 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7543 (m-10)
REVERT: I  664 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8050 (mm)
REVERT: I  686 TRP cc_start: 0.8167 (OUTLIER) cc_final: 0.7314 (t60)
REVERT: I  702 MET cc_start: 0.8925 (mmm) cc_final: 0.8678 (mmm)
REVERT: I  721 TYR cc_start: 0.7904 (m-80) cc_final: 0.7503 (m-10)
REVERT: K   12 ILE cc_start: 0.9247 (mt) cc_final: 0.8841 (mt)
REVERT: K   16 GLU cc_start: 0.9183 (tp30) cc_final: 0.8822 (mt-10)
REVERT: K   88 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8331 (mp0)
REVERT: K  107 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8516 (mm-40)
REVERT: K  113 ASP cc_start: 0.8805 (m-30) cc_final: 0.8572 (m-30)
REVERT: K  116 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8692 (tm-30)
REVERT: K  123 HIS cc_start: 0.9007 (t-90) cc_final: 0.8560 (t70)
REVERT: K  127 ILE cc_start: 0.9113 (tp) cc_final: 0.8787 (pt)
REVERT: K  128 MET cc_start: 0.9376 (tpp) cc_final: 0.9048 (tpp)
  outliers start: 21
  outliers final: 7
  residues processed: 173
  average time/residue: 0.0977
  time to fit residues: 20.9888
Evaluate side-chains
  128 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue   72 LEU
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  367 CYS
Chi-restraints excluded: chain I residue  390 ASN
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  597 VAL
Chi-restraints excluded: chain I residue  631 PHE
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  725 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** H   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 543 ASN
** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.072805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.060228 restraints weight = 23605.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.062306 restraints weight = 13407.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.063815 restraints weight = 9069.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.064864 restraints weight = 6758.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.065596 restraints weight = 5405.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5725  Z= 0.185
  Angle     :  0.756  13.684   7728  Z= 0.387
  Chirality :  0.044   0.309    886
  Planarity :  0.004   0.064    969
  Dihedral  :  5.607  26.519    735
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.66 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 20.53 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.32), residues: 679
  helix: -0.11 (0.24), residues: 465
  sheet:  None (None), residues: 0
  loop : -2.47 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K  82 
 TYR   0.011   0.002   TYR I 584 
 PHE   0.011   0.002   PHE K  72 
 TRP   0.010   0.002   TRP I 424 
 HIS   0.004   0.001   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 5725)
  covalent geometry    : angle       0.75597 ( 7728)
  hydrogen bonds       : bond        0.04578 (  321)
  hydrogen bonds       : angle       4.57670 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    7 LYS cc_start: 0.9390 (pptt) cc_final: 0.9138 (pptt)
REVERT: H   50 GLN cc_start: 0.8754 (tp40) cc_final: 0.8279 (tm-30)
REVERT: H   54 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8492 (mt-10)
REVERT: H   62 ASN cc_start: 0.8985 (t0) cc_final: 0.8444 (t0)
REVERT: H   64 GLU cc_start: 0.8660 (tt0) cc_final: 0.8424 (tt0)
REVERT: H   97 ASP cc_start: 0.8293 (m-30) cc_final: 0.7726 (m-30)
REVERT: H  118 ARG cc_start: 0.8769 (ttt90) cc_final: 0.8057 (tmm160)
REVERT: H  122 ASP cc_start: 0.8892 (t0) cc_final: 0.8683 (t0)
REVERT: I  296 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8079 (tt)
REVERT: I  337 LYS cc_start: 0.8786 (tttt) cc_final: 0.8223 (tttt)
REVERT: I  340 TYR cc_start: 0.8313 (m-10) cc_final: 0.7996 (m-10)
REVERT: I  352 GLU cc_start: 0.9263 (mp0) cc_final: 0.8767 (mm-30)
REVERT: I  358 GLU cc_start: 0.8304 (mp0) cc_final: 0.7957 (mp0)
REVERT: I  362 TRP cc_start: 0.8785 (t60) cc_final: 0.7373 (t60)
REVERT: I  366 ARG cc_start: 0.9158 (ptm160) cc_final: 0.8132 (ptm160)
REVERT: I  413 LEU cc_start: 0.9220 (tp) cc_final: 0.8965 (tt)
REVERT: I  417 CYS cc_start: 0.9006 (m) cc_final: 0.8544 (m)
REVERT: I  493 LEU cc_start: 0.9139 (mt) cc_final: 0.8806 (mt)
REVERT: I  498 ILE cc_start: 0.9262 (tt) cc_final: 0.8995 (pt)
REVERT: I  530 TYR cc_start: 0.6106 (p90) cc_final: 0.5902 (p90)
REVERT: I  549 ASP cc_start: 0.6860 (t0) cc_final: 0.6005 (t0)
REVERT: I  565 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8454 (ptmt)
REVERT: I  586 MET cc_start: 0.7929 (tmm) cc_final: 0.7587 (tmm)
REVERT: I  664 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7989 (mm)
REVERT: I  686 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7302 (t60)
REVERT: I  702 MET cc_start: 0.8897 (mmm) cc_final: 0.8680 (mmm)
REVERT: I  721 TYR cc_start: 0.8059 (m-80) cc_final: 0.7490 (m-10)
REVERT: K   16 GLU cc_start: 0.9137 (tp30) cc_final: 0.8842 (mt-10)
REVERT: K   61 MET cc_start: 0.8703 (mmm) cc_final: 0.8381 (mmm)
REVERT: K   78 PHE cc_start: 0.8312 (t80) cc_final: 0.7657 (t80)
REVERT: K   88 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8359 (mp0)
REVERT: K  113 ASP cc_start: 0.8806 (m-30) cc_final: 0.8557 (m-30)
REVERT: K  116 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8343 (tm-30)
REVERT: K  123 HIS cc_start: 0.9069 (t-90) cc_final: 0.8568 (t70)
REVERT: K  127 ILE cc_start: 0.9182 (tp) cc_final: 0.8830 (pt)
REVERT: K  128 MET cc_start: 0.9401 (tpp) cc_final: 0.8987 (tpp)
  outliers start: 25
  outliers final: 12
  residues processed: 151
  average time/residue: 0.0913
  time to fit residues: 17.6840
Evaluate side-chains
  142 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue   72 LEU
Chi-restraints excluded: chain I residue  296 LEU
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  367 CYS
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  707 THR
Chi-restraints excluded: chain I residue  711 TYR
Chi-restraints excluded: chain I residue  713 ASP
Chi-restraints excluded: chain I residue  725 LEU
Chi-restraints excluded: chain K residue   43 THR
Chi-restraints excluded: chain K residue   48 VAL
Chi-restraints excluded: chain K residue  126 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0270
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** H   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 390 ASN
** I 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.075017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.062148 restraints weight = 23027.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.064354 restraints weight = 13102.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.065904 restraints weight = 8796.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.067020 restraints weight = 6533.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.067813 restraints weight = 5195.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5725  Z= 0.139
  Angle     :  0.713  14.886   7728  Z= 0.360
  Chirality :  0.043   0.311    886
  Planarity :  0.004   0.043    969
  Dihedral  :  5.253  24.092    735
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 20.68 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.33), residues: 679
  helix:  0.35 (0.24), residues: 465
  sheet:  None (None), residues: 0
  loop : -2.31 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K  82 
 TYR   0.012   0.001   TYR I 584 
 PHE   0.013   0.001   PHE I 674 
 TRP   0.009   0.001   TRP I 686 
 HIS   0.004   0.001   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5725)
  covalent geometry    : angle       0.71287 ( 7728)
  hydrogen bonds       : bond        0.04070 (  321)
  hydrogen bonds       : angle       4.35620 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   24 ARG cc_start: 0.8972 (tpt-90) cc_final: 0.8606 (ttt-90)
REVERT: H   50 GLN cc_start: 0.8717 (tp40) cc_final: 0.8280 (tm-30)
REVERT: H  118 ARG cc_start: 0.8721 (ttt90) cc_final: 0.7916 (tmm160)
REVERT: I  296 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8083 (tt)
REVERT: I  337 LYS cc_start: 0.8827 (tttt) cc_final: 0.8134 (tttt)
REVERT: I  340 TYR cc_start: 0.8385 (m-10) cc_final: 0.8171 (m-10)
REVERT: I  352 GLU cc_start: 0.9302 (mp0) cc_final: 0.8799 (mm-30)
REVERT: I  358 GLU cc_start: 0.8378 (mp0) cc_final: 0.8013 (mp0)
REVERT: I  362 TRP cc_start: 0.8758 (t60) cc_final: 0.8406 (t60)
REVERT: I  390 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6914 (t0)
REVERT: I  413 LEU cc_start: 0.9208 (tp) cc_final: 0.8987 (tt)
REVERT: I  417 CYS cc_start: 0.9019 (m) cc_final: 0.8578 (m)
REVERT: I  493 LEU cc_start: 0.9098 (mt) cc_final: 0.8769 (mt)
REVERT: I  498 ILE cc_start: 0.9241 (tt) cc_final: 0.9002 (pt)
REVERT: I  549 ASP cc_start: 0.6922 (t0) cc_final: 0.6101 (t0)
REVERT: I  565 LYS cc_start: 0.8590 (tmtt) cc_final: 0.7669 (tppt)
REVERT: I  586 MET cc_start: 0.7908 (tmm) cc_final: 0.7460 (tmm)
REVERT: I  594 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6712 (ppt170)
REVERT: I  631 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7467 (m-10)
REVERT: I  664 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7938 (mm)
REVERT: I  686 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.7291 (t60)
REVERT: I  702 MET cc_start: 0.8905 (mmm) cc_final: 0.8669 (mmm)
REVERT: I  703 HIS cc_start: 0.8851 (t-90) cc_final: 0.8523 (t-90)
REVERT: I  721 TYR cc_start: 0.7987 (m-80) cc_final: 0.7477 (m-10)
REVERT: K   16 GLU cc_start: 0.9142 (tp30) cc_final: 0.8805 (mt-10)
REVERT: K   61 MET cc_start: 0.8745 (mmm) cc_final: 0.8385 (mmm)
REVERT: K   78 PHE cc_start: 0.8030 (t80) cc_final: 0.7357 (t80)
REVERT: K   88 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8317 (mp0)
REVERT: K  107 GLN cc_start: 0.8793 (mm-40) cc_final: 0.7985 (tm-30)
REVERT: K  113 ASP cc_start: 0.8818 (m-30) cc_final: 0.8555 (m-30)
REVERT: K  116 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: K  123 HIS cc_start: 0.9094 (t-90) cc_final: 0.8600 (t70)
REVERT: K  127 ILE cc_start: 0.9128 (tp) cc_final: 0.8765 (pt)
REVERT: K  128 MET cc_start: 0.9418 (tpp) cc_final: 0.8985 (tpp)
  outliers start: 25
  outliers final: 13
  residues processed: 160
  average time/residue: 0.0867
  time to fit residues: 17.6624
Evaluate side-chains
  141 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   72 LEU
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain I residue  296 LEU
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  367 CYS
Chi-restraints excluded: chain I residue  390 ASN
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  594 ARG
Chi-restraints excluded: chain I residue  597 VAL
Chi-restraints excluded: chain I residue  631 PHE
Chi-restraints excluded: chain I residue  639 LEU
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  684 HIS
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  695 ASP
Chi-restraints excluded: chain I residue  711 TYR
Chi-restraints excluded: chain I residue  725 LEU
Chi-restraints excluded: chain K residue   43 THR
Chi-restraints excluded: chain K residue  129 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0980
   chunk 52 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** H   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 ASN
** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.074453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.061300 restraints weight = 24050.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.063482 restraints weight = 13810.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.065031 restraints weight = 9373.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.066095 restraints weight = 7021.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.066914 restraints weight = 5641.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5725  Z= 0.148
  Angle     :  0.715  15.101   7728  Z= 0.362
  Chirality :  0.044   0.265    886
  Planarity :  0.004   0.047    969
  Dihedral  :  5.133  23.281    735
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 23.02 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.34), residues: 679
  helix:  0.49 (0.24), residues: 468
  sheet:  None (None), residues: 0
  loop : -2.05 (0.47), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  58 
 TYR   0.013   0.001   TYR I 593 
 PHE   0.013   0.001   PHE I 674 
 TRP   0.016   0.001   TRP K  89 
 HIS   0.005   0.001   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5725)
  covalent geometry    : angle       0.71518 ( 7728)
  hydrogen bonds       : bond        0.04087 (  321)
  hydrogen bonds       : angle       4.28160 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   24 ARG cc_start: 0.9011 (tpt-90) cc_final: 0.8589 (ttt-90)
REVERT: H  118 ARG cc_start: 0.8649 (ttt90) cc_final: 0.7934 (tmm160)
REVERT: I  296 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7970 (tt)
REVERT: I  337 LYS cc_start: 0.8893 (tttt) cc_final: 0.7900 (tttt)
REVERT: I  340 TYR cc_start: 0.8687 (m-10) cc_final: 0.8412 (m-10)
REVERT: I  352 GLU cc_start: 0.9307 (mp0) cc_final: 0.8790 (mm-30)
REVERT: I  358 GLU cc_start: 0.8389 (mp0) cc_final: 0.8022 (mp0)
REVERT: I  362 TRP cc_start: 0.8760 (t60) cc_final: 0.7440 (t60)
REVERT: I  366 ARG cc_start: 0.9152 (ptm160) cc_final: 0.8257 (ptm160)
REVERT: I  413 LEU cc_start: 0.9210 (tp) cc_final: 0.8998 (tt)
REVERT: I  417 CYS cc_start: 0.8960 (m) cc_final: 0.8498 (m)
REVERT: I  493 LEU cc_start: 0.9121 (mt) cc_final: 0.8785 (mt)
REVERT: I  549 ASP cc_start: 0.6814 (t0) cc_final: 0.6029 (t0)
REVERT: I  565 LYS cc_start: 0.8529 (tmtt) cc_final: 0.7781 (tptt)
REVERT: I  586 MET cc_start: 0.7955 (tmm) cc_final: 0.7639 (tmm)
REVERT: I  664 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7811 (mm)
REVERT: I  686 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7300 (t60)
REVERT: I  702 MET cc_start: 0.8860 (mmm) cc_final: 0.8623 (mmm)
REVERT: I  703 HIS cc_start: 0.8878 (t-90) cc_final: 0.8522 (t-90)
REVERT: K   16 GLU cc_start: 0.9136 (tp30) cc_final: 0.8788 (mt-10)
REVERT: K   61 MET cc_start: 0.8790 (mmm) cc_final: 0.8407 (mmm)
REVERT: K   78 PHE cc_start: 0.7992 (t80) cc_final: 0.7228 (t80)
REVERT: K   88 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8372 (mp0)
REVERT: K  107 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8005 (tm-30)
REVERT: K  113 ASP cc_start: 0.8826 (m-30) cc_final: 0.8558 (m-30)
REVERT: K  116 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8223 (tm-30)
REVERT: K  123 HIS cc_start: 0.9104 (t-90) cc_final: 0.8676 (t70)
REVERT: K  127 ILE cc_start: 0.9124 (tp) cc_final: 0.8756 (pt)
REVERT: K  128 MET cc_start: 0.9421 (tpp) cc_final: 0.8961 (tpp)
  outliers start: 22
  outliers final: 13
  residues processed: 147
  average time/residue: 0.0845
  time to fit residues: 15.9112
Evaluate side-chains
  139 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  129 ILE
Chi-restraints excluded: chain I residue  296 LEU
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  367 CYS
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  597 VAL
Chi-restraints excluded: chain I residue  639 LEU
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  684 HIS
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  695 ASP
Chi-restraints excluded: chain I residue  725 LEU
Chi-restraints excluded: chain K residue   43 THR
Chi-restraints excluded: chain K residue   81 LEU
Chi-restraints excluded: chain K residue  129 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 39 optimal weight:    0.1980
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** H   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 709 ASN
K 111 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.073648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.060572 restraints weight = 23714.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.062686 restraints weight = 13919.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.064186 restraints weight = 9542.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.065232 restraints weight = 7191.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.066029 restraints weight = 5793.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5725  Z= 0.171
  Angle     :  0.761  14.830   7728  Z= 0.378
  Chirality :  0.045   0.305    886
  Planarity :  0.004   0.052    969
  Dihedral  :  5.086  22.451    735
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 17.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 22.71 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.34), residues: 679
  helix:  0.52 (0.24), residues: 470
  sheet:  None (None), residues: 0
  loop : -1.99 (0.47), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  82 
 TYR   0.011   0.001   TYR I 584 
 PHE   0.015   0.002   PHE K  72 
 TRP   0.015   0.002   TRP K  89 
 HIS   0.004   0.001   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5725)
  covalent geometry    : angle       0.76092 ( 7728)
  hydrogen bonds       : bond        0.04026 (  321)
  hydrogen bonds       : angle       4.31641 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   24 ARG cc_start: 0.9027 (tpt-90) cc_final: 0.8622 (ttt-90)
REVERT: H   50 GLN cc_start: 0.8725 (tp40) cc_final: 0.8490 (tp40)
REVERT: H  118 ARG cc_start: 0.8687 (ttt90) cc_final: 0.7894 (tmm160)
REVERT: I  296 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7972 (tt)
REVERT: I  337 LYS cc_start: 0.8936 (tttt) cc_final: 0.7898 (tttt)
REVERT: I  340 TYR cc_start: 0.8585 (m-10) cc_final: 0.8305 (m-10)
REVERT: I  352 GLU cc_start: 0.9319 (mp0) cc_final: 0.8777 (mm-30)
REVERT: I  358 GLU cc_start: 0.8394 (mp0) cc_final: 0.8043 (mp0)
REVERT: I  362 TRP cc_start: 0.8742 (t60) cc_final: 0.8513 (t60)
REVERT: I  413 LEU cc_start: 0.9219 (tp) cc_final: 0.9006 (tt)
REVERT: I  417 CYS cc_start: 0.9046 (m) cc_final: 0.8622 (m)
REVERT: I  436 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8493 (t80)
REVERT: I  493 LEU cc_start: 0.9182 (mt) cc_final: 0.8785 (mt)
REVERT: I  522 LEU cc_start: 0.8907 (tp) cc_final: 0.8689 (tp)
REVERT: I  549 ASP cc_start: 0.6969 (t0) cc_final: 0.6203 (t0)
REVERT: I  586 MET cc_start: 0.7929 (tmm) cc_final: 0.7574 (tmm)
REVERT: I  594 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6311 (ppt170)
REVERT: I  664 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7779 (mm)
REVERT: I  686 TRP cc_start: 0.8297 (OUTLIER) cc_final: 0.7299 (t60)
REVERT: I  702 MET cc_start: 0.8837 (mmm) cc_final: 0.8582 (mmm)
REVERT: I  703 HIS cc_start: 0.8925 (t-90) cc_final: 0.8555 (t-90)
REVERT: K   16 GLU cc_start: 0.9158 (tp30) cc_final: 0.8790 (mt-10)
REVERT: K   61 MET cc_start: 0.8784 (mmm) cc_final: 0.8409 (mmm)
REVERT: K   78 PHE cc_start: 0.8073 (t80) cc_final: 0.7180 (t80)
REVERT: K   88 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8401 (mp0)
REVERT: K  107 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8073 (tm-30)
REVERT: K  113 ASP cc_start: 0.8855 (m-30) cc_final: 0.8580 (m-30)
REVERT: K  116 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: K  123 HIS cc_start: 0.9103 (t-90) cc_final: 0.8725 (t-90)
REVERT: K  127 ILE cc_start: 0.9148 (tp) cc_final: 0.8795 (pt)
REVERT: K  128 MET cc_start: 0.9409 (tpp) cc_final: 0.8961 (tpp)
  outliers start: 28
  outliers final: 14
  residues processed: 149
  average time/residue: 0.0857
  time to fit residues: 16.3846
Evaluate side-chains
  141 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  129 ILE
Chi-restraints excluded: chain I residue  296 LEU
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  367 CYS
Chi-restraints excluded: chain I residue  428 LEU
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  594 ARG
Chi-restraints excluded: chain I residue  597 VAL
Chi-restraints excluded: chain I residue  639 LEU
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  684 HIS
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  695 ASP
Chi-restraints excluded: chain I residue  707 THR
Chi-restraints excluded: chain I residue  725 LEU
Chi-restraints excluded: chain K residue   43 THR
Chi-restraints excluded: chain K residue   81 LEU
Chi-restraints excluded: chain K residue  129 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0170
   chunk 3 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 53 optimal weight:    0.2980
   chunk 59 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5620

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

Flipped N/Q/H residues before XYZ refinement:
H   8 GLN
I 390 ASN
I 471 ASN
K  14 ASN
K  18 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.076066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.062776 restraints weight = 23697.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.064980 restraints weight = 13865.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.066572 restraints weight = 9434.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.067695 restraints weight = 7047.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.068540 restraints weight = 5635.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5725  Z= 0.138
  Angle     :  0.751  14.805   7728  Z= 0.370
  Chirality :  0.044   0.311    886
  Planarity :  0.004   0.051    969
  Dihedral  :  4.909  21.535    735
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 24.73 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.34), residues: 679
  helix:  0.69 (0.25), residues: 470
  sheet:  None (None), residues: 0
  loop : -1.89 (0.47), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  37 
 TYR   0.014   0.001   TYR I 584 
 PHE   0.018   0.001   PHE I 611 
 TRP   0.014   0.001   TRP K  89 
 HIS   0.002   0.001   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5725)
  covalent geometry    : angle       0.75079 ( 7728)
  hydrogen bonds       : bond        0.03796 (  321)
  hydrogen bonds       : angle       4.15767 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   24 ARG cc_start: 0.8990 (tpt-90) cc_final: 0.8615 (ttt-90)
REVERT: H   41 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6589 (p90)
REVERT: H   50 GLN cc_start: 0.8738 (tp40) cc_final: 0.8468 (tp40)
REVERT: H   60 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7878 (tm-30)
REVERT: H  112 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8811 (mptt)
REVERT: H  118 ARG cc_start: 0.8577 (ttt90) cc_final: 0.7811 (tmm160)
REVERT: I  337 LYS cc_start: 0.8912 (tttt) cc_final: 0.7780 (tptt)
REVERT: I  352 GLU cc_start: 0.9312 (mp0) cc_final: 0.8894 (mm-30)
REVERT: I  413 LEU cc_start: 0.9253 (tp) cc_final: 0.9046 (tt)
REVERT: I  417 CYS cc_start: 0.8976 (m) cc_final: 0.8529 (m)
REVERT: I  436 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8389 (t80)
REVERT: I  549 ASP cc_start: 0.6858 (t0) cc_final: 0.6172 (t0)
REVERT: I  586 MET cc_start: 0.7946 (tmm) cc_final: 0.7557 (tmm)
REVERT: I  664 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7716 (mm)
REVERT: I  686 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7204 (t60)
REVERT: I  697 ARG cc_start: 0.8406 (mtt180) cc_final: 0.8202 (mtt180)
REVERT: I  702 MET cc_start: 0.8816 (mmm) cc_final: 0.8597 (mmm)
REVERT: I  703 HIS cc_start: 0.8878 (t-90) cc_final: 0.8580 (t-90)
REVERT: K   16 GLU cc_start: 0.9116 (tp30) cc_final: 0.8752 (mt-10)
REVERT: K   61 MET cc_start: 0.8804 (mmm) cc_final: 0.8409 (mmm)
REVERT: K   78 PHE cc_start: 0.8047 (t80) cc_final: 0.7145 (t80)
REVERT: K   88 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8493 (mp0)
REVERT: K   92 LEU cc_start: 0.8547 (mm) cc_final: 0.8319 (tt)
REVERT: K  107 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8094 (tm-30)
REVERT: K  113 ASP cc_start: 0.8814 (m-30) cc_final: 0.8539 (m-30)
REVERT: K  123 HIS cc_start: 0.9125 (t-90) cc_final: 0.8848 (t70)
REVERT: K  128 MET cc_start: 0.9423 (tpp) cc_final: 0.8974 (tpp)
  outliers start: 23
  outliers final: 12
  residues processed: 158
  average time/residue: 0.0803
  time to fit residues: 16.5537
Evaluate side-chains
  140 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   41 HIS
Chi-restraints excluded: chain H residue   48 THR
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  129 ILE
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  390 ASN
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  597 VAL
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  684 HIS
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  695 ASP
Chi-restraints excluded: chain I residue  707 THR
Chi-restraints excluded: chain I residue  725 LEU
Chi-restraints excluded: chain K residue   43 THR
Chi-restraints excluded: chain K residue   81 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0010
   chunk 64 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    0.4980
   chunk 46 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
I 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.076658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.063230 restraints weight = 23843.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.065421 restraints weight = 14199.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.066988 restraints weight = 9788.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.068078 restraints weight = 7385.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.068979 restraints weight = 5964.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5725  Z= 0.149
  Angle     :  0.826  16.700   7728  Z= 0.400
  Chirality :  0.046   0.337    886
  Planarity :  0.004   0.050    969
  Dihedral  :  4.900  20.160    735
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 26.59 %
    Favored  : 69.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.34), residues: 679
  helix:  0.76 (0.25), residues: 469
  sheet:  None (None), residues: 0
  loop : -1.88 (0.47), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K  82 
 TYR   0.037   0.002   TYR I 340 
 PHE   0.021   0.001   PHE K  72 
 TRP   0.039   0.002   TRP I 362 
 HIS   0.003   0.001   HIS H  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5725)
  covalent geometry    : angle       0.82553 ( 7728)
  hydrogen bonds       : bond        0.03963 (  321)
  hydrogen bonds       : angle       4.25965 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   24 ARG cc_start: 0.9034 (tpt-90) cc_final: 0.8639 (ttt-90)
REVERT: H   41 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6547 (p90)
REVERT: H   50 GLN cc_start: 0.8761 (tp40) cc_final: 0.8467 (tp40)
REVERT: H  112 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8853 (mptt)
REVERT: H  118 ARG cc_start: 0.8601 (ttt90) cc_final: 0.7829 (tmm160)
REVERT: I  337 LYS cc_start: 0.8847 (tttt) cc_final: 0.8230 (tptt)
REVERT: I  352 GLU cc_start: 0.9345 (mp0) cc_final: 0.9036 (mm-30)
REVERT: I  362 TRP cc_start: 0.8761 (t60) cc_final: 0.7036 (t60)
REVERT: I  366 ARG cc_start: 0.9080 (ptm160) cc_final: 0.8421 (ptm160)
REVERT: I  413 LEU cc_start: 0.9253 (tp) cc_final: 0.8979 (tp)
REVERT: I  417 CYS cc_start: 0.8937 (m) cc_final: 0.8474 (m)
REVERT: I  436 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8387 (t80)
REVERT: I  489 MET cc_start: 0.8697 (tpp) cc_final: 0.7540 (mmm)
REVERT: I  493 LEU cc_start: 0.9133 (mt) cc_final: 0.8739 (mt)
REVERT: I  549 ASP cc_start: 0.6974 (t0) cc_final: 0.6149 (t0)
REVERT: I  586 MET cc_start: 0.7787 (tmm) cc_final: 0.7568 (tmm)
REVERT: I  664 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7648 (mm)
REVERT: I  686 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.7151 (t60)
REVERT: I  697 ARG cc_start: 0.8406 (mtt180) cc_final: 0.8197 (mtt180)
REVERT: I  702 MET cc_start: 0.8769 (mmm) cc_final: 0.8563 (mmm)
REVERT: K   16 GLU cc_start: 0.9116 (tp30) cc_final: 0.8758 (mt-10)
REVERT: K   61 MET cc_start: 0.8819 (mmm) cc_final: 0.8403 (mmm)
REVERT: K   78 PHE cc_start: 0.8002 (t80) cc_final: 0.7085 (t80)
REVERT: K   88 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8446 (mp0)
REVERT: K  107 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8102 (tm-30)
REVERT: K  113 ASP cc_start: 0.8707 (m-30) cc_final: 0.8447 (m-30)
REVERT: K  116 GLU cc_start: 0.9197 (tp30) cc_final: 0.8882 (tp30)
REVERT: K  123 HIS cc_start: 0.9138 (t-90) cc_final: 0.8912 (t-90)
REVERT: K  128 MET cc_start: 0.9421 (tpp) cc_final: 0.8960 (tpp)
  outliers start: 26
  outliers final: 12
  residues processed: 151
  average time/residue: 0.0871
  time to fit residues: 16.9472
Evaluate side-chains
  138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   41 HIS
Chi-restraints excluded: chain H residue   48 THR
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  129 ILE
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  390 ASN
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  519 LEU
Chi-restraints excluded: chain I residue  597 VAL
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  684 HIS
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  695 ASP
Chi-restraints excluded: chain I residue  725 LEU
Chi-restraints excluded: chain K residue   43 THR
Chi-restraints excluded: chain K residue   81 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 45 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
I 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.077476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.064287 restraints weight = 23866.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.066496 restraints weight = 14091.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.068083 restraints weight = 9651.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.069231 restraints weight = 7236.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.070104 restraints weight = 5785.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5725  Z= 0.150
  Angle     :  0.859  17.338   7728  Z= 0.409
  Chirality :  0.046   0.255    886
  Planarity :  0.004   0.050    969
  Dihedral  :  4.872  20.282    735
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 26.44 %
    Favored  : 69.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.34), residues: 679
  helix:  0.79 (0.25), residues: 468
  sheet:  None (None), residues: 0
  loop : -1.86 (0.47), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I 433 
 TYR   0.018   0.001   TYR I 340 
 PHE   0.022   0.001   PHE I 674 
 TRP   0.028   0.002   TRP I 362 
 HIS   0.003   0.001   HIS I 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 5725)
  covalent geometry    : angle       0.85937 ( 7728)
  hydrogen bonds       : bond        0.03890 (  321)
  hydrogen bonds       : angle       4.30518 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.6478 (p90)
REVERT: H   50 GLN cc_start: 0.8761 (tp40) cc_final: 0.8457 (tp40)
REVERT: H  112 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8919 (mmtm)
REVERT: H  118 ARG cc_start: 0.8614 (ttt90) cc_final: 0.7806 (tmm160)
REVERT: I  337 LYS cc_start: 0.8860 (tttt) cc_final: 0.8555 (tptt)
REVERT: I  341 SER cc_start: 0.9622 (p) cc_final: 0.9398 (t)
REVERT: I  352 GLU cc_start: 0.9328 (mp0) cc_final: 0.9010 (mm-30)
REVERT: I  362 TRP cc_start: 0.8727 (t60) cc_final: 0.8248 (t60)
REVERT: I  390 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7684 (t0)
REVERT: I  413 LEU cc_start: 0.9255 (tp) cc_final: 0.8982 (tt)
REVERT: I  417 CYS cc_start: 0.8938 (m) cc_final: 0.8456 (m)
REVERT: I  549 ASP cc_start: 0.7029 (t0) cc_final: 0.6191 (t0)
REVERT: I  586 MET cc_start: 0.7742 (tmm) cc_final: 0.7529 (tmm)
REVERT: I  664 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7651 (mm)
REVERT: I  686 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.7186 (t60)
REVERT: I  702 MET cc_start: 0.8718 (mmm) cc_final: 0.8513 (mmm)
REVERT: K   16 GLU cc_start: 0.9107 (tp30) cc_final: 0.8729 (mt-10)
REVERT: K   61 MET cc_start: 0.8788 (mmm) cc_final: 0.8358 (mmm)
REVERT: K   78 PHE cc_start: 0.7968 (t80) cc_final: 0.6974 (t80)
REVERT: K   88 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8436 (mp0)
REVERT: K  113 ASP cc_start: 0.8665 (m-30) cc_final: 0.8426 (m-30)
REVERT: K  123 HIS cc_start: 0.9128 (t-90) cc_final: 0.8894 (t70)
REVERT: K  128 MET cc_start: 0.9420 (tpp) cc_final: 0.8954 (tpp)
  outliers start: 24
  outliers final: 15
  residues processed: 147
  average time/residue: 0.0885
  time to fit residues: 16.6629
Evaluate side-chains
  145 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   41 HIS
Chi-restraints excluded: chain H residue   48 THR
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  116 GLU
Chi-restraints excluded: chain H residue  129 ILE
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  390 ASN
Chi-restraints excluded: chain I residue  519 LEU
Chi-restraints excluded: chain I residue  597 VAL
Chi-restraints excluded: chain I residue  622 THR
Chi-restraints excluded: chain I residue  631 PHE
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  684 HIS
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  695 ASP
Chi-restraints excluded: chain I residue  721 TYR
Chi-restraints excluded: chain I residue  725 LEU
Chi-restraints excluded: chain K residue   43 THR
Chi-restraints excluded: chain K residue   81 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 12 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   chunk 44 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
I 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.077827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.064907 restraints weight = 23228.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.067165 restraints weight = 13440.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.068732 restraints weight = 9017.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.069859 restraints weight = 6689.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.070644 restraints weight = 5319.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5725  Z= 0.152
  Angle     :  0.889  17.003   7728  Z= 0.421
  Chirality :  0.047   0.235    886
  Planarity :  0.004   0.052    969
  Dihedral  :  4.915  21.073    735
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 27.22 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.34), residues: 679
  helix:  0.81 (0.25), residues: 468
  sheet:  None (None), residues: 0
  loop : -1.80 (0.48), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG K  58 
 TYR   0.017   0.002   TYR I 340 
 PHE   0.022   0.001   PHE I 674 
 TRP   0.022   0.002   TRP K  89 
 HIS   0.002   0.001   HIS H  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5725)
  covalent geometry    : angle       0.88929 ( 7728)
  hydrogen bonds       : bond        0.03894 (  321)
  hydrogen bonds       : angle       4.35570 (  951)

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

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

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1358 Ramachandran restraints generated.
    679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6391 (p90)
REVERT: H   50 GLN cc_start: 0.8723 (tp40) cc_final: 0.8428 (tp40)
REVERT: H  118 ARG cc_start: 0.8626 (ttt90) cc_final: 0.7783 (tmm160)
REVERT: I  337 LYS cc_start: 0.8829 (tttt) cc_final: 0.8557 (tptt)
REVERT: I  352 GLU cc_start: 0.9331 (mp0) cc_final: 0.9000 (mm-30)
REVERT: I  362 TRP cc_start: 0.8620 (t60) cc_final: 0.8024 (t60)
REVERT: I  365 LYS cc_start: 0.9151 (tmmt) cc_final: 0.8276 (tmmt)
REVERT: I  366 ARG cc_start: 0.9017 (mmp-170) cc_final: 0.8334 (mmp-170)
REVERT: I  390 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7730 (t0)
REVERT: I  413 LEU cc_start: 0.9226 (tp) cc_final: 0.8990 (tt)
REVERT: I  417 CYS cc_start: 0.8986 (m) cc_final: 0.8511 (m)
REVERT: I  489 MET cc_start: 0.8603 (tpp) cc_final: 0.7722 (mmm)
REVERT: I  549 ASP cc_start: 0.7005 (t0) cc_final: 0.6220 (t0)
REVERT: I  664 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7619 (mm)
REVERT: I  686 TRP cc_start: 0.8246 (OUTLIER) cc_final: 0.7223 (t60)
REVERT: K   16 GLU cc_start: 0.9126 (tp30) cc_final: 0.8729 (mt-10)
REVERT: K   58 ARG cc_start: 0.8759 (mtm110) cc_final: 0.8203 (mtm110)
REVERT: K   61 MET cc_start: 0.8762 (mmm) cc_final: 0.8347 (mmm)
REVERT: K   78 PHE cc_start: 0.7937 (t80) cc_final: 0.7016 (t80)
REVERT: K   88 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8393 (mp0)
REVERT: K  113 ASP cc_start: 0.8676 (m-30) cc_final: 0.8438 (m-30)
REVERT: K  116 GLU cc_start: 0.9110 (tp30) cc_final: 0.8909 (tp30)
REVERT: K  119 ARG cc_start: 0.9550 (ptm-80) cc_final: 0.9279 (ptm-80)
REVERT: K  123 HIS cc_start: 0.9132 (t-90) cc_final: 0.8885 (t70)
REVERT: K  128 MET cc_start: 0.9410 (tpp) cc_final: 0.8951 (tpp)
  outliers start: 20
  outliers final: 14
  residues processed: 143
  average time/residue: 0.0850
  time to fit residues: 15.6069
Evaluate side-chains
  140 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   41 HIS
Chi-restraints excluded: chain H residue   48 THR
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  129 ILE
Chi-restraints excluded: chain I residue  307 HIS
Chi-restraints excluded: chain I residue  390 ASN
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  519 LEU
Chi-restraints excluded: chain I residue  597 VAL
Chi-restraints excluded: chain I residue  622 THR
Chi-restraints excluded: chain I residue  664 ILE
Chi-restraints excluded: chain I residue  684 HIS
Chi-restraints excluded: chain I residue  686 TRP
Chi-restraints excluded: chain I residue  695 ASP
Chi-restraints excluded: chain I residue  721 TYR
Chi-restraints excluded: chain I residue  725 LEU
Chi-restraints excluded: chain K residue   43 THR
Chi-restraints excluded: chain K residue   81 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0980
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0870
   chunk 15 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
H  47 HIS
I 390 ASN
** I 666 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 = 0.3610 r_free = 0.3610 target = 0.078146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.065156 restraints weight = 23100.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.067355 restraints weight = 13544.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.068895 restraints weight = 9206.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.069995 restraints weight = 6896.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.070873 restraints weight = 5542.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5725  Z= 0.155
  Angle     :  0.895  17.254   7728  Z= 0.420
  Chirality :  0.046   0.228    886
  Planarity :  0.004   0.049    969
  Dihedral  :  4.935  21.794    735
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 28.62 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.34), residues: 679
  helix:  0.82 (0.25), residues: 468
  sheet:  None (None), residues: 0
  loop : -1.75 (0.48), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG K  58 
 TYR   0.016   0.002   TYR I 340 
 PHE   0.021   0.002   PHE I 674 
 TRP   0.016   0.002   TRP I 362 
 HIS   0.003   0.001   HIS I 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 5725)
  covalent geometry    : angle       0.89466 ( 7728)
  hydrogen bonds       : bond        0.03844 (  321)
  hydrogen bonds       : angle       4.36765 (  951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1337.74 seconds
wall clock time: 23 minutes 49.04 seconds (1429.04 seconds total)