Starting phenix.real_space_refine
on Tue Feb  3 20:31:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s4i_54565/02_2026/9s4i_54565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s4i_54565/02_2026/9s4i_54565.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s4i_54565/02_2026/9s4i_54565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s4i_54565/02_2026/9s4i_54565.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s4i_54565/02_2026/9s4i_54565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s4i_54565/02_2026/9s4i_54565.cif"
  }
  resolution = 4.0
  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=   0.019
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: 5
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     S      12      5.16       5
     C    4232      2.51       5
     N    1088      2.21       5
     O    1252      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6586
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1062
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1116
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 137}
    Chain: "C"
      Number of atoms: 2678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2678
          Classifications: {'peptide': 327}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 311}
    Chain: "D"
      Number of atoms: 1644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1644
          Classifications: {'peptide': 199}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 188}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.11, per 1000 atoms: 0.17
  Number of scatterers: 6586
  At special positions: 0
  Unit cell: (102.208, 95.2616, 119.077, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      2     26.01
     S      12     16.00
     O    1252      8.00
     N    1088      7.00
     C    4232      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 229.6 milliseconds
  

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      47.5% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 15
      removed outlier: 3.762A  pdb=" N   TRP A  14 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLY A  15 " --> pdb=" O   LYS A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 19
      removed outlier: 6.501A  pdb=" N   ALA A  19 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 16 through 19'
    Processing helix  chain 'A' and resid 20 through 36
      removed outlier: 3.558A  pdb=" N   TYR A  24 " --> pdb=" O   HIS A  20 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   MET A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 3.520A  pdb=" N   ALA A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 89
      removed outlier: 4.106A  pdb=" N   ASP A  85 " --> pdb=" O   SER A  81 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LEU A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 4.110A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   HIS A 112 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
      removed outlier: 3.639A  pdb=" N   SER A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 4.149A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 52 through 56
    Processing helix  chain 'B' and resid 57 through 75
    Processing helix  chain 'B' and resid 76 through 79
      removed outlier: 6.179A  pdb=" N   ASP B  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 76 through 79'
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
      removed outlier: 3.580A  pdb=" N   LYS B  95 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 119
      removed outlier: 3.914A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 141
    Processing helix  chain 'C' and resid 330 through 334
    Processing helix  chain 'C' and resid 364 through 369
    Processing helix  chain 'C' and resid 471 through 486
      Proline residue:  C 483  - end of helix
    Processing helix  chain 'C' and resid 489 through 503
      removed outlier: 3.542A  pdb=" N   GLU C 498 " --> pdb=" O   VAL C 494 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS C 499 " --> pdb=" O   TYR C 495 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 505 through 531
      removed outlier: 4.293A  pdb=" N   ALA C 510 " --> pdb=" O   GLU C 506 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   GLU C 511 " --> pdb=" O   LYS C 507 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR C 512 " --> pdb=" O   TYR C 508 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS C 514 " --> pdb=" O   ALA C 510 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL C 531 " --> pdb=" O   VAL C 527 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 565 through 569
    Processing helix  chain 'D' and resid 364 through 371
    Processing helix  chain 'D' and resid 471 through 487
      Proline residue:  D 483  - end of helix
      removed outlier: 3.790A  pdb=" N   ALA D 487 " --> pdb=" O   PRO D 483 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 489 through 502
      removed outlier: 3.778A  pdb=" N   GLU D 502 " --> pdb=" O   GLU D 498 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 505 through 507
      No H-bonds generated for 'chain 'D' and resid 505 through 507'
    Processing helix  chain 'D' and resid 508 through 529
      removed outlier: 4.107A  pdb=" N   TYR D 512 " --> pdb=" O   TYR D 508 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 349 through 352
      removed outlier: 6.461A  pdb=" N   TYR C 421 " --> pdb=" O   TYR C 415 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   TYR C 415 " --> pdb=" O   TYR C 421 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   TYR C 423 " --> pdb=" O   VAL C 413 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 354 through 357
      removed outlier: 4.423A  pdb=" N   TYR C 453 " --> pdb=" O   ILE C 437 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ILE C 437 " --> pdb=" O   TYR C 453 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   LEU C 455 " --> pdb=" O   VAL C 435 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL C 435 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLU C 442 " --> pdb=" O   TRP C 396 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   TRP C 396 " --> pdb=" O   GLU C 442 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 547 through 549
    Processing sheet with id=AA4, first strand: chain 'C' and resid 552 through 555
      removed outlier: 3.719A  pdb=" N   PHE C 555 " --> pdb=" O   ARG C 649 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG C 649 " --> pdb=" O   PHE C 555 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA C 631 " --> pdb=" O   VAL C 648 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASP C 596 " --> pdb=" O   LYS C 634 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   VAL C 636 " --> pdb=" O   TRP C 594 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   TRP C 594 " --> pdb=" O   VAL C 636 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 583 through 586
      removed outlier: 4.737A  pdb=" N   SER C 608 " --> pdb=" O   THR C 617 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ILE C 619 " --> pdb=" O   THR C 606 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   THR C 606 " --> pdb=" O   ILE C 619 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 349 through 352
      removed outlier: 3.856A  pdb=" N   SER D 414 " --> pdb=" O   TYR D 423 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ARG D 425 " --> pdb=" O   LEU D 412 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   LEU D 412 " --> pdb=" O   ARG D 425 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 354 through 357
      removed outlier: 4.633A  pdb=" N   TYR D 453 " --> pdb=" O   ILE D 437 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE D 437 " --> pdb=" O   TYR D 453 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   LEU D 455 " --> pdb=" O   VAL D 435 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL D 435 " --> pdb=" O   LEU D 455 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLU D 442 " --> pdb=" O   TRP D 396 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   TRP D 396 " --> pdb=" O   GLU D 442 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 354 through 357
      removed outlier: 4.633A  pdb=" N   TYR D 453 " --> pdb=" O   ILE D 437 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE D 437 " --> pdb=" O   TYR D 453 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   LEU D 455 " --> pdb=" O   VAL D 435 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL D 435 " --> pdb=" O   LEU D 455 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    894 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: 0.73

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 2790
        1.39 -     1.56: 3938
        1.56 -     1.73: 0
        1.73 -     1.90: 21
        1.90 -     2.06: 8
  Bond restraints: 6757
  Sorted by residual:
  bond pdb=" CA  SER C 394 "
       pdb=" CB  SER C 394 "
    ideal  model  delta    sigma   weight residual
    1.530  1.473  0.057 1.69e-02 3.50e+03 1.13e+01
  bond pdb=" N   LYS C 398 "
       pdb=" CA  LYS C 398 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.026 1.20e-02 6.94e+03 4.68e+00
  bond pdb=" N   LYS C 397 "
       pdb=" CA  LYS C 397 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.23e-02 6.61e+03 4.09e+00
  bond pdb=" N   ASP D 332 "
       pdb=" CA  ASP D 332 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.09e+00
  bond pdb=" N   LEU A   2 "
       pdb=" CA  LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.04e+00
  ... (remaining 6752 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 9084
        2.26 -     4.52: 105
        4.52 -     6.77: 7
        6.77 -     9.03: 1
        9.03 -    11.29: 2
  Bond angle restraints: 9199
  Sorted by residual:
  angle pdb=" CA  THR C 395 "
        pdb=" CB  THR C 395 "
        pdb=" OG1 THR C 395 "
      ideal   model   delta    sigma   weight residual
     109.60  103.84    5.76 1.50e+00 4.44e-01 1.48e+01
  angle pdb=" C   LYS C 397 "
        pdb=" CA  LYS C 397 "
        pdb=" CB  LYS C 397 "
      ideal   model   delta    sigma   weight residual
     110.85  104.52    6.33 1.70e+00 3.46e-01 1.39e+01
  angle pdb=" CA  LYS C 397 "
        pdb=" C   LYS C 397 "
        pdb=" O   LYS C 397 "
      ideal   model   delta    sigma   weight residual
     120.42  116.90    3.52 1.06e+00 8.90e-01 1.11e+01
  angle pdb=" N   SER C 394 "
        pdb=" CA  SER C 394 "
        pdb=" C   SER C 394 "
      ideal   model   delta    sigma   weight residual
     113.19  109.32    3.87 1.19e+00 7.06e-01 1.06e+01
  angle pdb=" N   VAL C 564 "
        pdb=" CA  VAL C 564 "
        pdb=" C   VAL C 564 "
      ideal   model   delta    sigma   weight residual
     113.00  109.55    3.45 1.30e+00 5.92e-01 7.03e+00
  ... (remaining 9194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3679
       17.96 -    35.92: 249
       35.92 -    53.88: 66
       53.88 -    71.84: 11
       71.84 -    89.80: 11
  Dihedral angle restraints: 4016
    sinusoidal: 1618
      harmonic: 2398
  Sorted by residual:
  dihedral pdb=" CA  GLN D 364 "
           pdb=" C   GLN D 364 "
           pdb=" N   PHE D 365 "
           pdb=" CA  PHE D 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.59  -18.41     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  LYS C 507 "
           pdb=" C   LYS C 507 "
           pdb=" N   TYR C 508 "
           pdb=" CA  TYR C 508 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.99   18.01     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" C1A HEM B 201 "
           pdb=" C2A HEM B 201 "
           pdb=" CAA HEM B 201 "
           pdb=" CBA HEM B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.80  -89.80     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 4013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 601
       0.030 -    0.060: 270
       0.060 -    0.090: 53
       0.090 -    0.120: 66
       0.120 -    0.150: 10
  Chirality restraints: 1000
  Sorted by residual:
  chirality pdb=" CA  ILE C 623 "
            pdb=" N   ILE C 623 "
            pdb=" C   ILE C 623 "
            pdb=" CB  ILE C 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.61e-01
  chirality pdb=" CB  VAL C 527 "
            pdb=" CA  VAL C 527 "
            pdb=" CG1 VAL C 527 "
            pdb=" CG2 VAL C 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.27e-01
  chirality pdb=" CA  VAL C 553 "
            pdb=" N   VAL C 553 "
            pdb=" C   VAL C 553 "
            pdb=" CB  VAL C 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 997 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 393 "   -0.011 2.00e-02 2.50e+03   2.10e-02 4.41e+00
        pdb=" C   ALA C 393 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ALA C 393 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER C 394 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 350 "   -0.034 5.00e-02 4.00e+02   5.11e-02 4.18e+00
        pdb=" N   PRO C 351 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO C 351 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 351 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 395 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.42e+00
        pdb=" C   THR C 395 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   THR C 395 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TRP C 396 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2182
        2.85 -     3.36: 6799
        3.36 -     3.87: 10338
        3.87 -     4.39: 11877
        4.39 -     4.90: 19815
  Nonbonded interactions: 51011
  Sorted by model distance:
  nonbonded pdb=" N   THR C 395 "
            pdb=" OG1 THR C 395 "
     model   vdw
     2.336 2.496
  nonbonded pdb=" O   ASN C 464 "
            pdb=" OD1 ASN C 464 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   LYS D 381 "
            pdb=" OG1 THR D 382 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" O   LYS C 391 "
            pdb=" OG1 THR C 392 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" O   PRO C 483 "
            pdb=" OE1 GLU C 496 "
     model   vdw
     2.463 3.040
  ... (remaining 51006 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=0.00 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.630
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.141   6759  Z= 0.151
  Angle     :  0.639  11.291   9199  Z= 0.344
  Chirality :  0.042   0.150   1000
  Planarity :  0.004   0.051   1174
  Dihedral  : 14.310  89.798   2468
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.09 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.31), residues: 803
  helix:  0.86 (0.29), residues: 320
  sheet: -0.55 (0.43), residues: 159
  loop : -0.17 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 492 
 TYR   0.015   0.001   TYR D 508 
 PHE   0.010   0.001   PHE A 117 
 TRP   0.018   0.002   TRP C 349 
 HIS   0.004   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6757)
  covalent geometry    : angle       0.63899 ( 9199)
  hydrogen bonds       : bond        0.18869 (  314)
  hydrogen bonds       : angle       7.18337 (  894)
  Misc. bond           : bond        0.13157 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 243
  time to evaluate  : 0.276 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 LEU cc_start: 0.9584 (mp) cc_final: 0.9353 (mp)
REVERT: B   41 PHE cc_start: 0.8338 (m-80) cc_final: 0.7721 (m-10)
REVERT: B   85 PHE cc_start: 0.8474 (m-80) cc_final: 0.8171 (m-80)
REVERT: B  108 ASN cc_start: 0.9648 (m-40) cc_final: 0.9343 (m-40)
REVERT: B  130 TYR cc_start: 0.8822 (m-80) cc_final: 0.8608 (m-80)
REVERT: C  360 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8562 (pttp)
REVERT: C  386 ILE cc_start: 0.8871 (mm) cc_final: 0.8571 (mm)
REVERT: C  446 ASN cc_start: 0.8822 (m110) cc_final: 0.8509 (t0)
REVERT: C  477 LEU cc_start: 0.9423 (tp) cc_final: 0.9210 (pp)
REVERT: C  525 ASP cc_start: 0.9184 (t0) cc_final: 0.8982 (m-30)
REVERT: C  596 ASP cc_start: 0.6522 (t0) cc_final: 0.4907 (t0)
REVERT: C  623 ILE cc_start: 0.8285 (mp) cc_final: 0.7656 (tp)
REVERT: D  356 MET cc_start: 0.8262 (mmm) cc_final: 0.7788 (mmm)
REVERT: D  478 GLN cc_start: 0.9093 (tt0) cc_final: 0.8884 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 244
  average time/residue: 0.0943
  time to fit residues: 28.6023
Evaluate side-chains
  119 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0040
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.3596

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A  78 ASN
A 103 HIS
B  63 HIS
B 143 HIS
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 355 GLN
** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.045212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.032986 restraints weight = 45687.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.034115 restraints weight = 32132.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.034923 restraints weight = 24682.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.035573 restraints weight = 20219.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.036058 restraints weight = 17243.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6759  Z= 0.168
  Angle     :  0.779   7.311   9199  Z= 0.401
  Chirality :  0.049   0.163   1000
  Planarity :  0.006   0.048   1174
  Dihedral  :  7.457  86.124    889
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.85 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.31), residues: 803
  helix:  1.04 (0.28), residues: 330
  sheet: -0.27 (0.43), residues: 160
  loop : -0.23 (0.39), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG C 425 
 TYR   0.013   0.001   TYR C 421 
 PHE   0.029   0.002   PHE D 365 
 TRP   0.020   0.002   TRP A  14 
 HIS   0.006   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6757)
  covalent geometry    : angle       0.77870 ( 9199)
  hydrogen bonds       : bond        0.04563 (  314)
  hydrogen bonds       : angle       5.77466 (  894)
  Misc. bond           : bond        0.03499 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.265 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8796 (pt0)
REVERT: A   60 LYS cc_start: 0.9535 (tptm) cc_final: 0.8936 (tptm)
REVERT: A   64 ASP cc_start: 0.9325 (m-30) cc_final: 0.8886 (m-30)
REVERT: A   76 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8724 (mmm)
REVERT: A   80 LEU cc_start: 0.9448 (mt) cc_final: 0.9191 (tp)
REVERT: A   92 ARG cc_start: 0.9528 (mpp80) cc_final: 0.9265 (mpp80)
REVERT: B   26 GLU cc_start: 0.9336 (tp30) cc_final: 0.9026 (tp30)
REVERT: B   40 ARG cc_start: 0.8989 (tmm-80) cc_final: 0.8782 (tmm-80)
REVERT: B   41 PHE cc_start: 0.8295 (m-80) cc_final: 0.7909 (m-10)
REVERT: B   85 PHE cc_start: 0.9426 (m-80) cc_final: 0.8535 (m-80)
REVERT: B  108 ASN cc_start: 0.9591 (m-40) cc_final: 0.9367 (m110)
REVERT: C  446 ASN cc_start: 0.9466 (m110) cc_final: 0.9163 (t0)
REVERT: C  496 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: C  525 ASP cc_start: 0.9710 (t0) cc_final: 0.9292 (m-30)
REVERT: C  552 PHE cc_start: 0.8874 (m-80) cc_final: 0.8147 (m-80)
REVERT: C  562 GLU cc_start: 0.9562 (mm-30) cc_final: 0.9350 (mm-30)
REVERT: C  565 MET cc_start: 0.9612 (mmm) cc_final: 0.9381 (mmm)
REVERT: C  586 MET cc_start: 0.8779 (tpt) cc_final: 0.8555 (tpt)
REVERT: D  364 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7500 (tm-30)
REVERT: D  478 GLN cc_start: 0.9266 (tt0) cc_final: 0.8905 (pt0)
REVERT: D  508 TYR cc_start: 0.8571 (t80) cc_final: 0.8271 (t80)
  outliers start: 17
  outliers final: 7
  residues processed: 139
  average time/residue: 0.0884
  time to fit residues: 15.7350
Evaluate side-chains
  113 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain D residue  493 GLN
Chi-restraints excluded: chain D residue  500 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0980
   chunk 8 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 446 ASN
** D 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.044354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.032271 restraints weight = 45564.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.033373 restraints weight = 32150.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.034207 restraints weight = 24837.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.034835 restraints weight = 20313.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.035304 restraints weight = 17388.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   6759  Z= 0.136
  Angle     :  0.703   7.135   9199  Z= 0.357
  Chirality :  0.047   0.169   1000
  Planarity :  0.005   0.052   1174
  Dihedral  :  7.148  89.585    889
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.99 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.31), residues: 803
  helix:  1.09 (0.29), residues: 330
  sheet: -0.28 (0.43), residues: 153
  loop : -0.18 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 433 
 TYR   0.018   0.001   TYR B  35 
 PHE   0.031   0.002   PHE D 365 
 TRP   0.010   0.001   TRP B  15 
 HIS   0.004   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6757)
  covalent geometry    : angle       0.70269 ( 9199)
  hydrogen bonds       : bond        0.03917 (  314)
  hydrogen bonds       : angle       5.28915 (  894)
  Misc. bond           : bond        0.05464 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.233 
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: A   27 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8938 (pt0)
REVERT: A   60 LYS cc_start: 0.9599 (tptm) cc_final: 0.9016 (tptm)
REVERT: A   64 ASP cc_start: 0.9262 (m-30) cc_final: 0.8797 (m-30)
REVERT: A   76 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8533 (mmm)
REVERT: A   92 ARG cc_start: 0.9481 (mpp80) cc_final: 0.9279 (mpp80)
REVERT: B   26 GLU cc_start: 0.9320 (tp30) cc_final: 0.8863 (tp30)
REVERT: B   41 PHE cc_start: 0.8398 (m-80) cc_final: 0.8129 (m-10)
REVERT: B   85 PHE cc_start: 0.9426 (m-80) cc_final: 0.8585 (m-80)
REVERT: B  108 ASN cc_start: 0.9573 (m-40) cc_final: 0.9312 (m-40)
REVERT: C  424 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9289 (tp)
REVERT: C  446 ASN cc_start: 0.9444 (m110) cc_final: 0.9149 (t0)
REVERT: C  492 ARG cc_start: 0.8759 (tpp80) cc_final: 0.8317 (tpp80)
REVERT: C  496 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7798 (mt-10)
REVERT: C  525 ASP cc_start: 0.9676 (t0) cc_final: 0.9227 (m-30)
REVERT: C  552 PHE cc_start: 0.8809 (m-80) cc_final: 0.8186 (m-80)
REVERT: C  565 MET cc_start: 0.9606 (mmm) cc_final: 0.9397 (mmm)
REVERT: C  573 PHE cc_start: 0.8738 (m-80) cc_final: 0.8520 (m-80)
REVERT: C  586 MET cc_start: 0.8836 (tpt) cc_final: 0.8047 (mmp)
REVERT: D  364 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7495 (tm-30)
REVERT: D  456 MET cc_start: 0.8834 (mmm) cc_final: 0.8618 (mmm)
REVERT: D  508 TYR cc_start: 0.8580 (t80) cc_final: 0.8192 (t80)
REVERT: D  517 ASP cc_start: 0.9496 (m-30) cc_final: 0.9240 (p0)
  outliers start: 21
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0816
  time to fit residues: 13.9311
Evaluate side-chains
  126 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   71 PHE
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain C residue  424 ILE
Chi-restraints excluded: chain C residue  500 LEU
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  625 ASP
Chi-restraints excluded: chain D residue  429 SER
Chi-restraints excluded: chain D residue  493 GLN
Chi-restraints excluded: chain D residue  500 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:   30.0000
   chunk 16 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
D 446 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.042769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.030972 restraints weight = 47992.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.032056 restraints weight = 33620.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.032832 restraints weight = 25913.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.033439 restraints weight = 21230.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.033896 restraints weight = 18212.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.4768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.131   6759  Z= 0.158
  Angle     :  0.701   7.714   9199  Z= 0.350
  Chirality :  0.046   0.192   1000
  Planarity :  0.005   0.053   1174
  Dihedral  :  6.962  81.077    889
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.99 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.31), residues: 803
  helix:  1.06 (0.29), residues: 330
  sheet: -0.55 (0.42), residues: 164
  loop : -0.24 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 433 
 TYR   0.028   0.002   TYR B 130 
 PHE   0.018   0.002   PHE D 365 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6757)
  covalent geometry    : angle       0.70091 ( 9199)
  hydrogen bonds       : bond        0.03700 (  314)
  hydrogen bonds       : angle       5.05611 (  894)
  Misc. bond           : bond        0.09946 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.279 
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: A   27 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9034 (pt0)
REVERT: A   60 LYS cc_start: 0.9625 (tptm) cc_final: 0.9061 (tptm)
REVERT: A   64 ASP cc_start: 0.9275 (m-30) cc_final: 0.8836 (m-30)
REVERT: A   76 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8518 (mmm)
REVERT: A   92 ARG cc_start: 0.9489 (mpp80) cc_final: 0.9271 (mpp80)
REVERT: B   21 ASP cc_start: 0.9022 (p0) cc_final: 0.8700 (p0)
REVERT: B   26 GLU cc_start: 0.9310 (tp30) cc_final: 0.9001 (tp30)
REVERT: B   85 PHE cc_start: 0.9472 (m-80) cc_final: 0.8674 (m-80)
REVERT: B  108 ASN cc_start: 0.9530 (m-40) cc_final: 0.9285 (m-40)
REVERT: C  492 ARG cc_start: 0.8831 (tpp80) cc_final: 0.8439 (tpp80)
REVERT: C  496 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7931 (mt-10)
REVERT: C  525 ASP cc_start: 0.9655 (t0) cc_final: 0.9218 (m-30)
REVERT: C  552 PHE cc_start: 0.8887 (m-80) cc_final: 0.7833 (m-80)
REVERT: C  565 MET cc_start: 0.9614 (mmm) cc_final: 0.9361 (mmm)
REVERT: C  588 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8557 (t)
REVERT: D  356 MET cc_start: 0.8569 (mmm) cc_final: 0.8026 (mmm)
REVERT: D  456 MET cc_start: 0.9060 (mmm) cc_final: 0.8558 (tpt)
REVERT: D  478 GLN cc_start: 0.9333 (tt0) cc_final: 0.8863 (mm110)
REVERT: D  508 TYR cc_start: 0.8799 (t80) cc_final: 0.8386 (t80)
  outliers start: 28
  outliers final: 14
  residues processed: 121
  average time/residue: 0.0698
  time to fit residues: 11.1755
Evaluate side-chains
  109 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain C residue  385 ILE
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  588 THR
Chi-restraints excluded: chain C residue  625 ASP
Chi-restraints excluded: chain D residue  352 ILE
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  429 SER
Chi-restraints excluded: chain D residue  500 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
D 446 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.042797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.031046 restraints weight = 47950.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.032127 restraints weight = 33345.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.032811 restraints weight = 25575.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.033490 restraints weight = 21155.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.033985 restraints weight = 18037.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.5005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111   6759  Z= 0.132
  Angle     :  0.668   6.812   9199  Z= 0.341
  Chirality :  0.046   0.174   1000
  Planarity :  0.005   0.053   1174
  Dihedral  :  6.980  82.013    889
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.41 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.31), residues: 803
  helix:  1.19 (0.30), residues: 323
  sheet: -0.65 (0.42), residues: 165
  loop : -0.16 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 433 
 TYR   0.023   0.001   TYR B 130 
 PHE   0.016   0.001   PHE D 365 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.006   0.001   HIS C 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6757)
  covalent geometry    : angle       0.66797 ( 9199)
  hydrogen bonds       : bond        0.03578 (  314)
  hydrogen bonds       : angle       4.94850 (  894)
  Misc. bond           : bond        0.08848 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.234 
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: A    7 LYS cc_start: 0.9529 (mtmt) cc_final: 0.9300 (mtmt)
REVERT: A   27 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9016 (pt0)
REVERT: A   60 LYS cc_start: 0.9624 (tptm) cc_final: 0.9079 (tptm)
REVERT: A   61 LYS cc_start: 0.9610 (mmmm) cc_final: 0.9323 (mtmt)
REVERT: A   64 ASP cc_start: 0.9283 (m-30) cc_final: 0.8846 (m-30)
REVERT: A   92 ARG cc_start: 0.9480 (mpp80) cc_final: 0.9230 (mpp80)
REVERT: A  126 ASP cc_start: 0.9172 (t70) cc_final: 0.8829 (m-30)
REVERT: B   26 GLU cc_start: 0.9337 (tp30) cc_final: 0.8913 (tp30)
REVERT: B   85 PHE cc_start: 0.9459 (m-80) cc_final: 0.8651 (m-80)
REVERT: C  492 ARG cc_start: 0.8826 (tpp80) cc_final: 0.8427 (tpp80)
REVERT: C  496 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7891 (mt-10)
REVERT: C  525 ASP cc_start: 0.9624 (t0) cc_final: 0.9196 (m-30)
REVERT: C  552 PHE cc_start: 0.8444 (m-80) cc_final: 0.7680 (m-80)
REVERT: C  588 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8566 (t)
REVERT: D  356 MET cc_start: 0.8455 (mmm) cc_final: 0.7722 (mmm)
REVERT: D  400 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8019 (mp0)
REVERT: D  456 MET cc_start: 0.8861 (mmm) cc_final: 0.8183 (tpt)
REVERT: D  478 GLN cc_start: 0.9335 (tt0) cc_final: 0.8853 (mm110)
REVERT: D  508 TYR cc_start: 0.8832 (t80) cc_final: 0.8457 (t80)
REVERT: D  517 ASP cc_start: 0.9492 (m-30) cc_final: 0.9274 (p0)
  outliers start: 21
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0732
  time to fit residues: 11.0208
Evaluate side-chains
  108 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain C residue  385 ILE
Chi-restraints excluded: chain C residue  531 VAL
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  588 THR
Chi-restraints excluded: chain C residue  625 ASP
Chi-restraints excluded: chain D residue  352 ILE
Chi-restraints excluded: chain D residue  400 GLU
Chi-restraints excluded: chain D residue  429 SER
Chi-restraints excluded: chain D residue  457 VAL
Chi-restraints excluded: chain D residue  500 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0050
   chunk 54 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 51 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.6002

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

Flipped N/Q/H residues before XYZ refinement:
D 446 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.040620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.029416 restraints weight = 49010.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.030417 restraints weight = 34239.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.031049 restraints weight = 26430.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.031685 restraints weight = 21932.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.032147 restraints weight = 18801.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.195   6759  Z= 0.202
  Angle     :  0.699   7.608   9199  Z= 0.355
  Chirality :  0.045   0.179   1000
  Planarity :  0.005   0.050   1174
  Dihedral  :  7.037  84.239    889
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.97 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.31), residues: 803
  helix:  1.19 (0.30), residues: 323
  sheet: -1.03 (0.41), residues: 175
  loop : -0.04 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 433 
 TYR   0.019   0.002   TYR B 130 
 PHE   0.020   0.002   PHE D 365 
 TRP   0.011   0.001   TRP A  14 
 HIS   0.008   0.001   HIS C 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 6757)
  covalent geometry    : angle       0.69894 ( 9199)
  hydrogen bonds       : bond        0.03612 (  314)
  hydrogen bonds       : angle       4.94864 (  894)
  Misc. bond           : bond        0.16231 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9000 (pt0)
REVERT: A   60 LYS cc_start: 0.9629 (tptm) cc_final: 0.9063 (tptm)
REVERT: A   64 ASP cc_start: 0.9297 (m-30) cc_final: 0.8931 (m-30)
REVERT: A   92 ARG cc_start: 0.9465 (mpp80) cc_final: 0.9221 (mpp80)
REVERT: A  126 ASP cc_start: 0.9232 (t70) cc_final: 0.8908 (m-30)
REVERT: B   26 GLU cc_start: 0.9361 (tp30) cc_final: 0.8879 (tp30)
REVERT: B   85 PHE cc_start: 0.9495 (m-80) cc_final: 0.8696 (m-80)
REVERT: B  108 ASN cc_start: 0.9484 (m-40) cc_final: 0.9242 (m-40)
REVERT: C  492 ARG cc_start: 0.8879 (tpp80) cc_final: 0.8660 (tpp80)
REVERT: C  525 ASP cc_start: 0.9611 (t0) cc_final: 0.9155 (m-30)
REVERT: C  552 PHE cc_start: 0.8575 (m-80) cc_final: 0.7838 (m-80)
REVERT: C  588 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8094 (t)
REVERT: D  356 MET cc_start: 0.8461 (mmm) cc_final: 0.7874 (mmm)
REVERT: D  456 MET cc_start: 0.8973 (mmm) cc_final: 0.8652 (mmm)
REVERT: D  478 GLN cc_start: 0.9367 (tt0) cc_final: 0.8909 (mm110)
REVERT: D  508 TYR cc_start: 0.8866 (t80) cc_final: 0.8512 (t80)
  outliers start: 26
  outliers final: 19
  residues processed: 104
  average time/residue: 0.0808
  time to fit residues: 11.2886
Evaluate side-chains
  99 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue    9 ASN
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain C residue  385 ILE
Chi-restraints excluded: chain C residue  531 VAL
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  588 THR
Chi-restraints excluded: chain C residue  625 ASP
Chi-restraints excluded: chain D residue  352 ILE
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  417 SER
Chi-restraints excluded: chain D residue  457 VAL
Chi-restraints excluded: chain D residue  500 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7758

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

Flipped N/Q/H residues before XYZ refinement:
D 446 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.041911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.030402 restraints weight = 47761.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.031484 restraints weight = 33105.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.032291 restraints weight = 25320.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.032888 restraints weight = 20586.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.033349 restraints weight = 17540.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.5476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.137   6759  Z= 0.129
  Angle     :  0.705  11.340   9199  Z= 0.351
  Chirality :  0.046   0.168   1000
  Planarity :  0.005   0.052   1174
  Dihedral  :  6.937  83.934    889
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.38 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.31), residues: 803
  helix:  1.09 (0.30), residues: 323
  sheet: -0.92 (0.40), residues: 176
  loop : -0.06 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 104 
 TYR   0.012   0.001   TYR D 366 
 PHE   0.013   0.001   PHE D 365 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6757)
  covalent geometry    : angle       0.70479 ( 9199)
  hydrogen bonds       : bond        0.03410 (  314)
  hydrogen bonds       : angle       4.85228 (  894)
  Misc. bond           : bond        0.11140 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9013 (pt0)
REVERT: A   64 ASP cc_start: 0.9265 (m-30) cc_final: 0.8987 (m-30)
REVERT: A   92 ARG cc_start: 0.9411 (mpp80) cc_final: 0.9173 (mpp80)
REVERT: B   14 LEU cc_start: 0.9554 (mm) cc_final: 0.9344 (pp)
REVERT: B   26 GLU cc_start: 0.9331 (tp30) cc_final: 0.8972 (tp30)
REVERT: B   85 PHE cc_start: 0.9481 (m-80) cc_final: 0.8662 (m-80)
REVERT: B  108 ASN cc_start: 0.9521 (m-40) cc_final: 0.8936 (m-40)
REVERT: C  492 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8636 (tpp80)
REVERT: C  525 ASP cc_start: 0.9611 (t0) cc_final: 0.9148 (m-30)
REVERT: C  552 PHE cc_start: 0.8488 (m-80) cc_final: 0.7714 (m-80)
REVERT: D  478 GLN cc_start: 0.9346 (tt0) cc_final: 0.8883 (pt0)
REVERT: D  508 TYR cc_start: 0.8905 (t80) cc_final: 0.8531 (t80)
REVERT: D  517 ASP cc_start: 0.9538 (m-30) cc_final: 0.9303 (p0)
  outliers start: 17
  outliers final: 13
  residues processed: 103
  average time/residue: 0.0642
  time to fit residues: 9.1623
Evaluate side-chains
  99 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue  385 ILE
Chi-restraints excluded: chain C residue  531 VAL
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  625 ASP
Chi-restraints excluded: chain D residue  429 SER
Chi-restraints excluded: chain D residue  446 ASN
Chi-restraints excluded: chain D residue  457 VAL
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  500 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 61 optimal weight:    8.9990
   chunk 67 optimal weight:    0.0070
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
D 448 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.042132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.030645 restraints weight = 47946.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.031727 restraints weight = 33170.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.032532 restraints weight = 25381.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.033121 restraints weight = 20648.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.033592 restraints weight = 17597.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.5630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   6759  Z= 0.126
  Angle     :  0.690   9.908   9199  Z= 0.343
  Chirality :  0.045   0.176   1000
  Planarity :  0.005   0.052   1174
  Dihedral  :  6.957  83.397    889
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.52 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.31), residues: 803
  helix:  1.07 (0.30), residues: 322
  sheet: -0.83 (0.41), residues: 176
  loop : -0.08 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 104 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.027   0.001   PHE D 365 
 TRP   0.007   0.001   TRP C 594 
 HIS   0.003   0.001   HIS C 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6757)
  covalent geometry    : angle       0.68956 ( 9199)
  hydrogen bonds       : bond        0.03375 (  314)
  hydrogen bonds       : angle       4.77594 (  894)
  Misc. bond           : bond        0.09118 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9010 (pt0)
REVERT: B   26 GLU cc_start: 0.9315 (tp30) cc_final: 0.8928 (tp30)
REVERT: B   85 PHE cc_start: 0.9498 (m-80) cc_final: 0.8674 (m-80)
REVERT: B  108 ASN cc_start: 0.9384 (m-40) cc_final: 0.9078 (m-40)
REVERT: B  113 VAL cc_start: 0.9175 (t) cc_final: 0.8931 (t)
REVERT: C  492 ARG cc_start: 0.8903 (tpp80) cc_final: 0.8696 (tpp80)
REVERT: C  525 ASP cc_start: 0.9603 (t0) cc_final: 0.9139 (m-30)
REVERT: C  552 PHE cc_start: 0.8429 (m-80) cc_final: 0.7596 (m-80)
REVERT: D  350 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8389 (ttm-80)
REVERT: D  356 MET cc_start: 0.8433 (mmm) cc_final: 0.7535 (mmm)
REVERT: D  517 ASP cc_start: 0.9533 (m-30) cc_final: 0.9289 (p0)
  outliers start: 22
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0699
  time to fit residues: 10.4300
Evaluate side-chains
  106 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain C residue  385 ILE
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  531 VAL
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  625 ASP
Chi-restraints excluded: chain D residue  350 ARG
Chi-restraints excluded: chain D residue  429 SER
Chi-restraints excluded: chain D residue  457 VAL
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  500 LEU
Chi-restraints excluded: chain D residue  516 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 53 optimal weight:    0.3980
   chunk 76 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 66 optimal weight:    8.9990
   chunk 51 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D 446 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.042253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.030775 restraints weight = 48016.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.031849 restraints weight = 33633.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.032620 restraints weight = 25854.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.033224 restraints weight = 21231.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.033685 restraints weight = 18074.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.5725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   6759  Z= 0.130
  Angle     :  0.722   9.935   9199  Z= 0.365
  Chirality :  0.046   0.165   1000
  Planarity :  0.005   0.075   1174
  Dihedral  :  6.969  83.459    889
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.94 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.31), residues: 803
  helix:  0.95 (0.30), residues: 327
  sheet: -0.86 (0.41), residues: 176
  loop : -0.01 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 104 
 TYR   0.013   0.001   TYR D 366 
 PHE   0.025   0.002   PHE D 365 
 TRP   0.010   0.001   TRP B  15 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6757)
  covalent geometry    : angle       0.72172 ( 9199)
  hydrogen bonds       : bond        0.03493 (  314)
  hydrogen bonds       : angle       4.84008 (  894)
  Misc. bond           : bond        0.08188 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8998 (pt0)
REVERT: A   43 PHE cc_start: 0.9265 (m-80) cc_final: 0.8630 (m-80)
REVERT: A   92 ARG cc_start: 0.9275 (mpp80) cc_final: 0.9064 (mpp80)
REVERT: B   26 GLU cc_start: 0.9309 (tp30) cc_final: 0.8918 (tp30)
REVERT: B   85 PHE cc_start: 0.9504 (m-80) cc_final: 0.8687 (m-80)
REVERT: B  108 ASN cc_start: 0.9407 (m-40) cc_final: 0.9158 (m-40)
REVERT: C  456 MET cc_start: 0.9668 (tpp) cc_final: 0.9441 (mmm)
REVERT: C  525 ASP cc_start: 0.9608 (t0) cc_final: 0.9167 (m-30)
REVERT: C  552 PHE cc_start: 0.8373 (m-80) cc_final: 0.7535 (m-80)
REVERT: D  350 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8390 (ttm-80)
REVERT: D  365 PHE cc_start: 0.8832 (t80) cc_final: 0.8559 (t80)
REVERT: D  456 MET cc_start: 0.9048 (tpt) cc_final: 0.8798 (mmm)
REVERT: D  500 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8929 (pp)
REVERT: D  517 ASP cc_start: 0.9524 (m-30) cc_final: 0.9279 (p0)
  outliers start: 19
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0661
  time to fit residues: 9.9380
Evaluate side-chains
  108 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  478 GLN
Chi-restraints excluded: chain C residue  531 VAL
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  625 ASP
Chi-restraints excluded: chain D residue  350 ARG
Chi-restraints excluded: chain D residue  446 ASN
Chi-restraints excluded: chain D residue  457 VAL
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  500 LEU
Chi-restraints excluded: chain D residue  516 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 35 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0570
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
D 446 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.042613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.031160 restraints weight = 47665.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.032218 restraints weight = 33211.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.033014 restraints weight = 25576.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.033630 restraints weight = 20925.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.034077 restraints weight = 17835.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.5863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088   6759  Z= 0.136
  Angle     :  0.781  12.073   9199  Z= 0.390
  Chirality :  0.047   0.165   1000
  Planarity :  0.005   0.075   1174
  Dihedral  :  6.991  83.983    889
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.37 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.31), residues: 803
  helix:  0.93 (0.29), residues: 327
  sheet: -0.83 (0.41), residues: 174
  loop : -0.07 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 104 
 TYR   0.013   0.001   TYR D 366 
 PHE   0.023   0.001   PHE D 365 
 TRP   0.008   0.001   TRP B  15 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6757)
  covalent geometry    : angle       0.78093 ( 9199)
  hydrogen bonds       : bond        0.03581 (  314)
  hydrogen bonds       : angle       4.93218 (  894)
  Misc. bond           : bond        0.06744 (    2)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9007 (pt0)
REVERT: A   43 PHE cc_start: 0.9245 (m-80) cc_final: 0.8637 (m-80)
REVERT: A   92 ARG cc_start: 0.9248 (mpp80) cc_final: 0.9030 (mpp80)
REVERT: B   26 GLU cc_start: 0.9271 (tp30) cc_final: 0.8860 (tp30)
REVERT: B   85 PHE cc_start: 0.9507 (m-80) cc_final: 0.8672 (m-80)
REVERT: B  108 ASN cc_start: 0.9350 (m-40) cc_final: 0.9030 (m-40)
REVERT: C  456 MET cc_start: 0.9650 (tpp) cc_final: 0.9051 (tpp)
REVERT: C  525 ASP cc_start: 0.9613 (t0) cc_final: 0.9180 (m-30)
REVERT: C  552 PHE cc_start: 0.8311 (m-80) cc_final: 0.7490 (m-80)
REVERT: D  350 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8443 (ttm-80)
REVERT: D  500 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8920 (pp)
REVERT: D  516 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9334 (mm)
REVERT: D  517 ASP cc_start: 0.9526 (m-30) cc_final: 0.9275 (p0)
  outliers start: 18
  outliers final: 14
  residues processed: 104
  average time/residue: 0.0667
  time to fit residues: 9.6719
Evaluate side-chains
  105 residues out of total 707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue    9 ASN
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  478 GLN
Chi-restraints excluded: chain C residue  531 VAL
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  625 ASP
Chi-restraints excluded: chain D residue  350 ARG
Chi-restraints excluded: chain D residue  446 ASN
Chi-restraints excluded: chain D residue  457 VAL
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  500 LEU
Chi-restraints excluded: chain D residue  516 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 34 optimal weight:    0.0270
   chunk 38 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0070
   chunk 1 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 69 optimal weight:    5.9990
   overall best weight:    0.5256

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

Flipped N/Q/H residues before XYZ refinement:
D 446 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.042834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.031353 restraints weight = 47813.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.032413 restraints weight = 33367.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.033204 restraints weight = 25716.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.033811 restraints weight = 21104.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.034282 restraints weight = 18010.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.5939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   6759  Z= 0.135
  Angle     :  0.765  11.621   9199  Z= 0.384
  Chirality :  0.046   0.189   1000
  Planarity :  0.005   0.052   1174
  Dihedral  :  6.987  84.788    889
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.65 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.31), residues: 803
  helix:  0.91 (0.29), residues: 326
  sheet: -0.85 (0.41), residues: 174
  loop : -0.09 (0.38), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 104 
 TYR   0.011   0.001   TYR D 366 
 PHE   0.037   0.001   PHE D 365 
 TRP   0.006   0.001   TRP B  15 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6757)
  covalent geometry    : angle       0.76525 ( 9199)
  hydrogen bonds       : bond        0.03652 (  314)
  hydrogen bonds       : angle       4.94968 (  894)
  Misc. bond           : bond        0.05950 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1133.54 seconds
wall clock time: 20 minutes 20.88 seconds (1220.88 seconds total)