Starting phenix.real_space_refine
on Thu Sep 18 00:28:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cvc_45959/09_2025/9cvc_45959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cvc_45959/09_2025/9cvc_45959.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cvc_45959/09_2025/9cvc_45959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cvc_45959/09_2025/9cvc_45959.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cvc_45959/09_2025/9cvc_45959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cvc_45959/09_2025/9cvc_45959.map"
  }
  resolution = 3.5
  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=  -0.001 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    8054      2.51       5
     N    2146      2.21       5
     O    2313      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12564
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4543
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 34, 'TRANS': 535}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 4253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 534, 4253
          Classifications: {'peptide': 534}
          Link IDs: {'PTRANS': 29, 'TRANS': 504}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 1256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1256
          Classifications: {'peptide': 156}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 143}
    Chain: "D"
      Number of atoms: 1256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1256
          Classifications: {'peptide': 156}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 143}
    Chain: "E"
      Number of atoms: 1256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1256
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 12, 'TRANS': 143}
  Time building chain proxies: 3.70, per 1000 atoms: 0.29
  Number of scatterers: 12564
  At special positions: 0
  Unit cell: (88.275, 127.875, 142.725, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    2313      8.00
     N    2146      7.00
     C    8054      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 632.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2986

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 9 sheets defined
      52.5% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 14 through 23
    Processing helix  chain 'A' and resid 32 through 43
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    Processing helix  chain 'A' and resid 48 through 62
    Processing helix  chain 'A' and resid 206 through 210
    Processing helix  chain 'A' and resid 298 through 315
    Processing helix  chain 'A' and resid 320 through 333
    Processing helix  chain 'A' and resid 362 through 377
      removed outlier: 3.987A  pdb=" N   CYS A 376 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   HIS A 377 " --> pdb=" O   VAL A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 385 through 395
    Processing helix  chain 'A' and resid 395 through 402
      removed outlier: 3.754A  pdb=" N   LEU A 399 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 419
    Processing helix  chain 'A' and resid 446 through 469
    Processing helix  chain 'A' and resid 476 through 495
      removed outlier: 5.646A  pdb=" N   SER A 483 " --> pdb=" O   LYS A 479 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ARG A 484 " --> pdb=" O   GLY A 480 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 495 " --> pdb=" O   GLN A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 514
      removed outlier: 3.558A  pdb=" N   GLN A 514 " --> pdb=" O   LEU A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 550
    Processing helix  chain 'A' and resid 566 through 579
      removed outlier: 3.911A  pdb=" N   PHE A 570 " --> pdb=" O   GLY A 566 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE A 571 " --> pdb=" O   CYS A 567 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER A 579 " --> pdb=" O   ILE A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 600
    Processing helix  chain 'A' and resid 615 through 645
      removed outlier: 3.746A  pdb=" N   PHE A 645 " --> pdb=" O   GLY A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 675 through 686
    Processing helix  chain 'A' and resid 688 through 701
      Proline residue:  A 694  - end of helix
    Processing helix  chain 'A' and resid 710 through 726
    Processing helix  chain 'A' and resid 738 through 754
    Processing helix  chain 'A' and resid 759 through 764
      removed outlier: 4.237A  pdb=" N   PHE A 763 " --> pdb=" O   PRO A 759 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   PHE A 764 " --> pdb=" O   GLU A 760 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 759 through 764'
    Processing helix  chain 'A' and resid 791 through 799
    Processing helix  chain 'A' and resid 802 through 818
      removed outlier: 4.038A  pdb=" N   ARG A 806 " --> pdb=" O   ILE A 802 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 10
    Processing helix  chain 'B' and resid 14 through 23
    Processing helix  chain 'B' and resid 32 through 43
    Processing helix  chain 'B' and resid 44 through 46
      No H-bonds generated for 'chain 'B' and resid 44 through 46'
    Processing helix  chain 'B' and resid 48 through 62
    Processing helix  chain 'B' and resid 298 through 315
    Processing helix  chain 'B' and resid 320 through 333
    Processing helix  chain 'B' and resid 362 through 377
      removed outlier: 3.958A  pdb=" N   CYS B 376 " --> pdb=" O   GLN B 372 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS B 377 " --> pdb=" O   VAL B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 383
    Processing helix  chain 'B' and resid 385 through 395
    Processing helix  chain 'B' and resid 395 through 402
      removed outlier: 3.681A  pdb=" N   LEU B 399 " --> pdb=" O   ASN B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 419
    Processing helix  chain 'B' and resid 446 through 469
    Processing helix  chain 'B' and resid 476 through 495
      removed outlier: 5.625A  pdb=" N   SER B 483 " --> pdb=" O   LYS B 479 " (cutoff:3.500A)
      removed outlier: 5.815A  pdb=" N   ARG B 484 " --> pdb=" O   GLY B 480 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA B 495 " --> pdb=" O   GLN B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 514
    Processing helix  chain 'B' and resid 536 through 550
    Processing helix  chain 'B' and resid 566 through 579
      removed outlier: 3.928A  pdb=" N   PHE B 570 " --> pdb=" O   GLY B 566 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE B 571 " --> pdb=" O   CYS B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 600
    Processing helix  chain 'B' and resid 615 through 645
      removed outlier: 3.690A  pdb=" N   TRP B 619 " --> pdb=" O   SER B 615 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN B 620 " --> pdb=" O   ASP B 616 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE B 645 " --> pdb=" O   GLY B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 668
    Processing helix  chain 'B' and resid 675 through 687
    Processing helix  chain 'B' and resid 688 through 701
      Proline residue:  B 694  - end of helix
    Processing helix  chain 'B' and resid 710 through 726
    Processing helix  chain 'B' and resid 738 through 754
    Processing helix  chain 'B' and resid 783 through 787
    Processing helix  chain 'B' and resid 791 through 799
    Processing helix  chain 'B' and resid 802 through 818
      removed outlier: 4.126A  pdb=" N   ARG B 806 " --> pdb=" O   ILE B 802 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 54
      removed outlier: 3.824A  pdb=" N   TYR C  53 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 91
      removed outlier: 4.433A  pdb=" N   VAL C  90 " --> pdb=" O   ASP C  86 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLY C  91 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 86 through 91'
    Processing helix  chain 'C' and resid 119 through 125
      removed outlier: 3.599A  pdb=" N   ARG C 123 " --> pdb=" O   GLU C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 133
      No H-bonds generated for 'chain 'C' and resid 131 through 133'
    Processing helix  chain 'D' and resid 86 through 91
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.508A  pdb=" N   ARG D 123 " --> pdb=" O   GLU D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 52
      No H-bonds generated for 'chain 'E' and resid 50 through 52'
    Processing helix  chain 'E' and resid 86 through 91
      removed outlier: 4.033A  pdb=" N   VAL E  90 " --> pdb=" O   ASP E  86 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLY E  91 " --> pdb=" O   ALA E  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 86 through 91'
    Processing helix  chain 'E' and resid 119 through 125
    Processing helix  chain 'E' and resid 131 through 133
      No H-bonds generated for 'chain 'E' and resid 131 through 133'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 11
      removed outlier: 5.010A  pdb=" N   THR C  27 " --> pdb=" O   ASN C   7 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   VAL C   9 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   GLU C  25 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 11
      removed outlier: 5.010A  pdb=" N   THR C  27 " --> pdb=" O   ASN C   7 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   VAL C   9 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   GLU C  25 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 16 through 17
      removed outlier: 3.548A  pdb=" N   ILE C  42 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ASP C  58 " --> pdb=" O   ILE C  42 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   TYR C  44 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   VAL C  56 " --> pdb=" O   TYR C  44 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 16 through 17
      removed outlier: 6.935A  pdb=" N   CYS C  99 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 12
      removed outlier: 6.603A  pdb=" N   THR D  27 " --> pdb=" O   ASN D   7 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   VAL D   9 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   GLU D  25 " --> pdb=" O   VAL D   9 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   VAL D  11 " --> pdb=" O   GLN D  23 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   GLN D  23 " --> pdb=" O   VAL D  11 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 55 through 62
      removed outlier: 5.610A  pdb=" N   VAL D  56 " --> pdb=" O   TYR D  44 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   TYR D  44 " --> pdb=" O   VAL D  56 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASP D  58 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 11
      removed outlier: 4.575A  pdb=" N   THR E  27 " --> pdb=" O   ASN E   7 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   VAL E   9 " --> pdb=" O   GLU E  25 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   GLU E  25 " --> pdb=" O   VAL E   9 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 15 through 17
      removed outlier: 5.240A  pdb=" N   VAL E  94 " --> pdb=" O   VAL E  45 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL E  45 " --> pdb=" O   VAL E  94 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   LEU E  38 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LEU E  61 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   TRP E  40 " --> pdb=" O   SER E  59 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   SER E  59 " --> pdb=" O   TRP E  40 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ILE E  42 " --> pdb=" O   LEU E  57 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 15 through 17
      removed outlier: 6.753A  pdb=" N   CYS E  99 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)

    641 hydrogen bonds defined for protein.
    1857 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: 2.15

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2716
        1.33 -     1.45: 2856
        1.45 -     1.57: 7213
        1.57 -     1.69: 0
        1.69 -     1.82: 73
  Bond restraints: 12858
  Sorted by residual:
  bond pdb=" CG  LEU C 135 "
       pdb=" CD1 LEU C 135 "
    ideal  model  delta    sigma   weight residual
    1.521  1.438  0.083 3.30e-02 9.18e+02 6.39e+00
  bond pdb=" N   SER A 207 "
       pdb=" CA  SER A 207 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.22e+00
  bond pdb=" CG1 ILE B 755 "
       pdb=" CD1 ILE B 755 "
    ideal  model  delta    sigma   weight residual
    1.513  1.420  0.093 3.90e-02 6.57e+02 5.71e+00
  bond pdb=" N   LEU A 208 "
       pdb=" CA  LEU A 208 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.33e-02 5.65e+03 5.49e+00
  bond pdb=" N   LYS A 210 "
       pdb=" CA  LYS A 210 "
    ideal  model  delta    sigma   weight residual
    1.451  1.486 -0.035 1.60e-02 3.91e+03 4.86e+00
  ... (remaining 12853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 16794
        1.57 -     3.13: 513
        3.13 -     4.70: 131
        4.70 -     6.27: 18
        6.27 -     7.84: 6
  Bond angle restraints: 17462
  Sorted by residual:
  angle pdb=" CA  GLU B 732 "
        pdb=" CB  GLU B 732 "
        pdb=" CG  GLU B 732 "
      ideal   model   delta    sigma   weight residual
     114.10  121.09   -6.99 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" CA  PRO D  21 "
        pdb=" N   PRO D  21 "
        pdb=" CD  PRO D  21 "
      ideal   model   delta    sigma   weight residual
     112.00  107.30    4.70 1.40e+00 5.10e-01 1.13e+01
  angle pdb=" N   GLU A  59 "
        pdb=" CA  GLU A  59 "
        pdb=" CB  GLU A  59 "
      ideal   model   delta    sigma   weight residual
     110.07  114.94   -4.87 1.45e+00 4.76e-01 1.13e+01
  angle pdb=" CA  ARG D 108 "
        pdb=" CB  ARG D 108 "
        pdb=" CG  ARG D 108 "
      ideal   model   delta    sigma   weight residual
     114.10  120.60   -6.50 2.00e+00 2.50e-01 1.06e+01
  angle pdb=" N   LEU A 208 "
        pdb=" CA  LEU A 208 "
        pdb=" C   LEU A 208 "
      ideal   model   delta    sigma   weight residual
     112.54  108.69    3.85 1.22e+00 6.72e-01 9.95e+00
  ... (remaining 17457 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 6970
       17.86 -    35.72: 631
       35.72 -    53.59: 89
       53.59 -    71.45: 31
       71.45 -    89.31: 14
  Dihedral angle restraints: 7735
    sinusoidal: 3157
      harmonic: 4578
  Sorted by residual:
  dihedral pdb=" CA  ALA B 495 "
           pdb=" C   ALA B 495 "
           pdb=" N   CYS B 496 "
           pdb=" CA  CYS B 496 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.67   17.33     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ALA A 495 "
           pdb=" C   ALA A 495 "
           pdb=" N   CYS A 496 "
           pdb=" CA  CYS A 496 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.12   16.88     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  GLY A 480 "
           pdb=" C   GLY A 480 "
           pdb=" N   LEU A 481 "
           pdb=" CA  LEU A 481 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.61  -16.39     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 7732 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1534
       0.049 -    0.098: 308
       0.098 -    0.147: 91
       0.147 -    0.196: 8
       0.196 -    0.246: 2
  Chirality restraints: 1943
  Sorted by residual:
  chirality pdb=" CG  LEU D  38 "
            pdb=" CB  LEU D  38 "
            pdb=" CD1 LEU D  38 "
            pdb=" CD2 LEU D  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.84    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  ILE C  97 "
            pdb=" N   ILE C  97 "
            pdb=" C   ILE C  97 "
            pdb=" CB  ILE C  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  ILE C  42 "
            pdb=" N   ILE C  42 "
            pdb=" C   ILE C  42 "
            pdb=" CB  ILE C  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.64e-01
  ... (remaining 1940 not shown)

  Planarity restraints: 2286
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  20 "   -0.088 5.00e-02 4.00e+02   1.31e-01 2.74e+01
        pdb=" N   PRO D  21 "    0.226 5.00e-02 4.00e+02
        pdb=" CA  PRO D  21 "   -0.070 5.00e-02 4.00e+02
        pdb=" CD  PRO D  21 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 758 "    0.073 5.00e-02 4.00e+02   1.10e-01 1.93e+01
        pdb=" N   PRO B 759 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO B 759 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO B 759 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  16 "   -0.062 5.00e-02 4.00e+02   9.37e-02 1.41e+01
        pdb=" N   PRO D  17 "    0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO D  17 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO D  17 "   -0.051 5.00e-02 4.00e+02
  ... (remaining 2283 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 198
        2.61 -     3.18: 12177
        3.18 -     3.76: 19210
        3.76 -     4.33: 25517
        4.33 -     4.90: 42820
  Nonbonded interactions: 99922
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 385 "
            pdb=" N   LYS A 386 "
     model   vdw
     2.041 3.120
  nonbonded pdb=" O   SER B 444 "
            pdb=" OG  SER B 445 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" O   PRO D  21 "
            pdb=" OE1 GLN D  23 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" OE2 GLU E  39 "
            pdb=" OG  SER E  59 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" OH  TYR A 648 "
            pdb=" OD2 ASP B 589 "
     model   vdw
     2.146 3.040
  ... (remaining 99917 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 68 or resid 285 through 419 or resid 439 through \ 
 766 or resid 782 through 818))
  selection = (chain 'B' and resid 2 through 818)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.230
  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:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     13.520
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
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   0.093  12858  Z= 0.171
  Angle     :  0.688   7.837  17462  Z= 0.371
  Chirality :  0.044   0.246   1943
  Planarity :  0.007   0.131   2286
  Dihedral  : 14.295  89.310   4749
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.41 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.22), residues: 1538
  helix:  1.18 (0.20), residues: 737
  sheet: -1.67 (0.38), residues: 207
  loop : -1.06 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A  58 
 TYR   0.030   0.002   TYR C 111 
 PHE   0.023   0.002   PHE B 443 
 TRP   0.017   0.002   TRP B  21 
 HIS   0.007   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (12858)
  covalent geometry    : angle       0.68800 (17462)
  hydrogen bonds       : bond        0.13619 (  618)
  hydrogen bonds       : angle       6.07326 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7042 (tt0)
REVERT: A  463 LEU cc_start: 0.7840 (tp) cc_final: 0.7521 (tp)
REVERT: A  652 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7224 (tm-30)
REVERT: A  751 TRP cc_start: 0.8436 (t60) cc_final: 0.7614 (t60)
REVERT: C   29 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6470 (tm-30)
REVERT: D   26 ILE cc_start: 0.8432 (mp) cc_final: 0.8169 (mp)
REVERT: D   96 LEU cc_start: 0.8073 (pp) cc_final: 0.7756 (tt)
REVERT: D  101 TYR cc_start: 0.6947 (t80) cc_final: 0.6522 (t80)
REVERT: E  113 VAL cc_start: 0.7279 (t) cc_final: 0.7059 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.1057
  time to fit residues: 37.6350
Evaluate side-chains
  173 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0370
   chunk 149 optimal weight:    0.5980
   overall best weight:    0.9062

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

Flipped N/Q/H residues before XYZ refinement:
A 491 GLN
A 599 ASN
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D   7 ASN
D  20 ASN
E 138 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.167743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.125168 restraints weight = 26636.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.128764 restraints weight = 14103.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.131157 restraints weight = 9818.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.132583 restraints weight = 7995.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.133161 restraints weight = 7136.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12858  Z= 0.166
  Angle     :  0.692   9.965  17462  Z= 0.353
  Chirality :  0.044   0.170   1943
  Planarity :  0.005   0.068   2286
  Dihedral  :  4.054  18.026   1693
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.14 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.22), residues: 1538
  helix:  1.72 (0.19), residues: 747
  sheet: -1.13 (0.39), residues: 197
  loop : -1.17 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 667 
 TYR   0.015   0.002   TYR C  53 
 PHE   0.031   0.002   PHE D 106 
 TRP   0.016   0.002   TRP E  40 
 HIS   0.006   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (12858)
  covalent geometry    : angle       0.69233 (17462)
  hydrogen bonds       : bond        0.04614 (  618)
  hydrogen bonds       : angle       4.69326 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7358 (tp30)
REVERT: A  652 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7278 (tm-30)
REVERT: A  751 TRP cc_start: 0.8679 (t60) cc_final: 0.8203 (t60)
REVERT: B   52 PHE cc_start: 0.7339 (t80) cc_final: 0.7019 (t80)
REVERT: B  318 VAL cc_start: 0.7852 (m) cc_final: 0.7641 (t)
REVERT: C   29 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6717 (tm-30)
REVERT: C   74 PHE cc_start: 0.6140 (t80) cc_final: 0.5830 (t80)
REVERT: C  136 GLN cc_start: 0.6734 (tp-100) cc_final: 0.6183 (tp40)
REVERT: D   23 GLN cc_start: 0.7509 (mp10) cc_final: 0.7225 (mp10)
REVERT: D  111 TYR cc_start: 0.8100 (m-80) cc_final: 0.7341 (m-10)
REVERT: E  113 VAL cc_start: 0.7297 (t) cc_final: 0.7070 (m)
  outliers start: 20
  outliers final: 12
  residues processed: 196
  average time/residue: 0.0920
  time to fit residues: 27.2234
Evaluate side-chains
  158 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue   98 THR
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue  122 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 142 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 148 optimal weight:    0.2980
   chunk 112 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 47 optimal weight:    0.5980
   chunk 100 optimal weight:    0.5980
   chunk 122 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 669 GLN
B 455 GLN
B 491 GLN
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  55 GLN
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   5 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.167435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.127309 restraints weight = 26723.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.129494 restraints weight = 14640.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.131806 restraints weight = 10111.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.132059 restraints weight = 8722.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.131852 restraints weight = 7737.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12858  Z= 0.133
  Angle     :  0.637  11.269  17462  Z= 0.317
  Chirality :  0.041   0.151   1943
  Planarity :  0.004   0.059   2286
  Dihedral  :  3.983  17.515   1693
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.94 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.22), residues: 1538
  helix:  1.92 (0.19), residues: 752
  sheet: -1.05 (0.37), residues: 212
  loop : -1.24 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 667 
 TYR   0.018   0.001   TYR A 648 
 PHE   0.022   0.002   PHE D 106 
 TRP   0.011   0.001   TRP B 695 
 HIS   0.003   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12858)
  covalent geometry    : angle       0.63657 (17462)
  hydrogen bonds       : bond        0.03978 (  618)
  hydrogen bonds       : angle       4.44411 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 MET cc_start: 0.6027 (mmm) cc_final: 0.5654 (mmm)
REVERT: A  461 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7245 (mt-10)
REVERT: A  652 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7249 (tm-30)
REVERT: B   52 PHE cc_start: 0.7311 (t80) cc_final: 0.6928 (t80)
REVERT: C   29 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6608 (tm-30)
REVERT: D   23 GLN cc_start: 0.7524 (mp10) cc_final: 0.7212 (mp10)
REVERT: D   41 LYS cc_start: 0.8742 (tttm) cc_final: 0.8488 (tttm)
REVERT: D  111 TYR cc_start: 0.8063 (m-80) cc_final: 0.7351 (m-10)
  outliers start: 23
  outliers final: 14
  residues processed: 181
  average time/residue: 0.0822
  time to fit residues: 23.1345
Evaluate side-chains
  166 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue   97 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 117 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0060
   chunk 10 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   5 GLN
E   7 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.168418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.125422 restraints weight = 26847.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.129379 restraints weight = 13605.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.131986 restraints weight = 9295.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.133470 restraints weight = 7491.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.134080 restraints weight = 6650.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12858  Z= 0.129
  Angle     :  0.617  13.784  17462  Z= 0.305
  Chirality :  0.040   0.149   1943
  Planarity :  0.005   0.054   2286
  Dihedral  :  3.896  17.695   1693
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.59 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.22), residues: 1538
  helix:  1.95 (0.19), residues: 755
  sheet: -0.84 (0.38), residues: 212
  loop : -1.21 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 667 
 TYR   0.021   0.001   TYR A 648 
 PHE   0.021   0.002   PHE A  56 
 TRP   0.012   0.002   TRP D  40 
 HIS   0.004   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (12858)
  covalent geometry    : angle       0.61653 (17462)
  hydrogen bonds       : bond        0.03753 (  618)
  hydrogen bonds       : angle       4.25188 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 167
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.8252 (mm) cc_final: 0.8022 (mp)
REVERT: A  337 MET cc_start: 0.5985 (mmm) cc_final: 0.5685 (mmm)
REVERT: A  461 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7222 (mt-10)
REVERT: A  652 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7130 (tm-30)
REVERT: B   52 PHE cc_start: 0.7309 (t80) cc_final: 0.7023 (t80)
REVERT: C    1 MET cc_start: 0.2968 (mmp) cc_final: 0.2647 (mmt)
REVERT: C   29 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6469 (tm-30)
REVERT: D    5 GLN cc_start: 0.8367 (mp10) cc_final: 0.8051 (mp10)
REVERT: D   23 GLN cc_start: 0.7476 (mp10) cc_final: 0.7211 (mp10)
REVERT: D   96 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7902 (tt)
REVERT: D  145 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7427 (ttp80)
  outliers start: 29
  outliers final: 15
  residues processed: 185
  average time/residue: 0.0885
  time to fit residues: 25.1614
Evaluate side-chains
  168 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue   12 LEU
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue   97 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 53 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 129 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   chunk 22 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 130 optimal weight:   10.0000
   chunk 119 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 136 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.167977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.124916 restraints weight = 27048.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.128935 restraints weight = 13760.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.131542 restraints weight = 9376.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.132923 restraints weight = 7563.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.133553 restraints weight = 6736.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12858  Z= 0.126
  Angle     :  0.616  12.572  17462  Z= 0.300
  Chirality :  0.041   0.197   1943
  Planarity :  0.004   0.053   2286
  Dihedral  :  3.847  18.341   1693
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.53 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.22), residues: 1538
  helix:  1.98 (0.19), residues: 757
  sheet: -0.82 (0.37), residues: 216
  loop : -1.20 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 667 
 TYR   0.017   0.001   TYR C 111 
 PHE   0.029   0.002   PHE B 443 
 TRP   0.012   0.001   TRP B 695 
 HIS   0.004   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12858)
  covalent geometry    : angle       0.61565 (17462)
  hydrogen bonds       : bond        0.03590 (  618)
  hydrogen bonds       : angle       4.14677 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.8253 (mm) cc_final: 0.8032 (mp)
REVERT: A  337 MET cc_start: 0.5944 (mmm) cc_final: 0.5705 (mmm)
REVERT: A  461 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7206 (mt-10)
REVERT: A  652 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7107 (tm-30)
REVERT: B   52 PHE cc_start: 0.7314 (t80) cc_final: 0.6967 (t80)
REVERT: C    1 MET cc_start: 0.2903 (mmp) cc_final: 0.2645 (mmt)
REVERT: C   29 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6327 (tm-30)
REVERT: C  136 GLN cc_start: 0.7250 (tp-100) cc_final: 0.6615 (tp40)
REVERT: D   23 GLN cc_start: 0.7623 (mp10) cc_final: 0.7229 (mp10)
REVERT: D   29 GLU cc_start: 0.8615 (pt0) cc_final: 0.8274 (mm-30)
REVERT: D   96 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7944 (tt)
REVERT: D  111 TYR cc_start: 0.8304 (m-10) cc_final: 0.7781 (m-10)
REVERT: D  145 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7398 (ttp80)
  outliers start: 24
  outliers final: 16
  residues processed: 179
  average time/residue: 0.0851
  time to fit residues: 23.6528
Evaluate side-chains
  165 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue   97 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 121 optimal weight:    0.8980
   chunk 146 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 133 optimal weight:    2.9990
   chunk 154 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 406 GLN
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.164058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.122987 restraints weight = 26461.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.125367 restraints weight = 14870.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.127870 restraints weight = 10300.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.127950 restraints weight = 8934.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.127688 restraints weight = 8014.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12858  Z= 0.153
  Angle     :  0.619  12.548  17462  Z= 0.305
  Chirality :  0.041   0.178   1943
  Planarity :  0.005   0.054   2286
  Dihedral  :  3.893  17.509   1693
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.89 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.22), residues: 1538
  helix:  1.93 (0.19), residues: 751
  sheet: -0.76 (0.37), residues: 212
  loop : -1.24 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 137 
 TYR   0.015   0.001   TYR C 111 
 PHE   0.033   0.002   PHE B 626 
 TRP   0.012   0.001   TRP B 695 
 HIS   0.006   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12858)
  covalent geometry    : angle       0.61920 (17462)
  hydrogen bonds       : bond        0.03762 (  618)
  hydrogen bonds       : angle       4.08052 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 160
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7838 (mp0)
REVERT: A  317 LEU cc_start: 0.8338 (mm) cc_final: 0.8108 (mp)
REVERT: A  337 MET cc_start: 0.5970 (mmm) cc_final: 0.5736 (mmm)
REVERT: A  461 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7318 (tp30)
REVERT: A  652 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: B   52 PHE cc_start: 0.7357 (t80) cc_final: 0.6959 (t80)
REVERT: C    1 MET cc_start: 0.3048 (mmp) cc_final: 0.2844 (mmm)
REVERT: C    8 ASN cc_start: 0.7390 (p0) cc_final: 0.6690 (t0)
REVERT: C   43 ILE cc_start: 0.7595 (mm) cc_final: 0.7394 (mm)
REVERT: C  136 GLN cc_start: 0.7381 (tp-100) cc_final: 0.6967 (tp40)
REVERT: D   23 GLN cc_start: 0.7701 (mp10) cc_final: 0.7249 (mp10)
REVERT: D   29 GLU cc_start: 0.8647 (pt0) cc_final: 0.8329 (mm-30)
REVERT: D   96 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7950 (tt)
REVERT: D  111 TYR cc_start: 0.8369 (m-10) cc_final: 0.7843 (m-10)
REVERT: D  145 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7381 (ttp80)
  outliers start: 32
  outliers final: 21
  residues processed: 180
  average time/residue: 0.0842
  time to fit residues: 23.8491
Evaluate side-chains
  172 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  406 GLN
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  497 SER
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  139 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 149 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9990
   chunk 137 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 153 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 553 GLN
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 143 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.164655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.122388 restraints weight = 26234.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.125919 restraints weight = 13955.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.128213 restraints weight = 9734.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.129549 restraints weight = 7938.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.130038 restraints weight = 7074.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12858  Z= 0.128
  Angle     :  0.627  14.174  17462  Z= 0.301
  Chirality :  0.040   0.169   1943
  Planarity :  0.005   0.056   2286
  Dihedral  :  3.873  18.414   1693
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.90 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.22), residues: 1538
  helix:  1.92 (0.19), residues: 759
  sheet: -0.78 (0.37), residues: 212
  loop : -1.16 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 123 
 TYR   0.020   0.001   TYR B 713 
 PHE   0.022   0.002   PHE D 106 
 TRP   0.013   0.001   TRP B 695 
 HIS   0.004   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (12858)
  covalent geometry    : angle       0.62660 (17462)
  hydrogen bonds       : bond        0.03614 (  618)
  hydrogen bonds       : angle       4.02814 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7785 (mp0)
REVERT: A  317 LEU cc_start: 0.8276 (mm) cc_final: 0.8042 (mp)
REVERT: A  461 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7303 (tp30)
REVERT: A  652 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7096 (tm-30)
REVERT: C    8 ASN cc_start: 0.7359 (p0) cc_final: 0.6593 (t0)
REVERT: C  136 GLN cc_start: 0.7422 (tp-100) cc_final: 0.6857 (tp-100)
REVERT: D   23 GLN cc_start: 0.7711 (mp10) cc_final: 0.7244 (mp10)
REVERT: D   29 GLU cc_start: 0.8558 (pt0) cc_final: 0.8244 (mm-30)
REVERT: D   96 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7898 (tt)
REVERT: D  111 TYR cc_start: 0.8317 (m-10) cc_final: 0.7760 (m-10)
REVERT: D  112 TYR cc_start: 0.6857 (m-80) cc_final: 0.6649 (m-10)
REVERT: E   66 PRO cc_start: 0.8085 (Cg_exo) cc_final: 0.7801 (Cg_endo)
  outliers start: 26
  outliers final: 21
  residues processed: 175
  average time/residue: 0.0872
  time to fit residues: 23.6487
Evaluate side-chains
  178 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  443 PHE
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  656 THR
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  106 PHE
Chi-restraints excluded: chain E residue  139 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 150 optimal weight:    8.9990
   chunk 59 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 112 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 406 GLN
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 143 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.164248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.127370 restraints weight = 26397.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.128485 restraints weight = 15075.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.128882 restraints weight = 11466.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.129263 restraints weight = 10057.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.129467 restraints weight = 9579.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12858  Z= 0.135
  Angle     :  0.628  14.022  17462  Z= 0.303
  Chirality :  0.041   0.162   1943
  Planarity :  0.005   0.054   2286
  Dihedral  :  3.852  17.588   1693
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.19 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.22), residues: 1538
  helix:  1.92 (0.19), residues: 759
  sheet: -0.75 (0.37), residues: 212
  loop : -1.18 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 447 
 TYR   0.023   0.001   TYR B 713 
 PHE   0.025   0.002   PHE A  56 
 TRP   0.013   0.001   TRP B 695 
 HIS   0.005   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12858)
  covalent geometry    : angle       0.62813 (17462)
  hydrogen bonds       : bond        0.03527 (  618)
  hydrogen bonds       : angle       3.98043 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.8243 (mm) cc_final: 0.8040 (mp)
REVERT: A  337 MET cc_start: 0.6521 (mmm) cc_final: 0.5946 (mmm)
REVERT: A  461 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7299 (tp30)
REVERT: A  652 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7311 (tm-30)
REVERT: C    8 ASN cc_start: 0.7394 (p0) cc_final: 0.6585 (t0)
REVERT: C  136 GLN cc_start: 0.7377 (tp-100) cc_final: 0.6828 (tp-100)
REVERT: D   23 GLN cc_start: 0.7677 (mp10) cc_final: 0.7204 (mp10)
REVERT: D   29 GLU cc_start: 0.8312 (pt0) cc_final: 0.8110 (mm-30)
REVERT: D   96 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7774 (tt)
REVERT: D  111 TYR cc_start: 0.7519 (m-10) cc_final: 0.6946 (m-10)
REVERT: D  112 TYR cc_start: 0.6550 (m-80) cc_final: 0.6289 (m-10)
REVERT: E   66 PRO cc_start: 0.7840 (Cg_exo) cc_final: 0.7582 (Cg_endo)
  outliers start: 31
  outliers final: 20
  residues processed: 178
  average time/residue: 0.0985
  time to fit residues: 27.1702
Evaluate side-chains
  169 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  443 PHE
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  497 SER
Chi-restraints excluded: chain B residue  656 THR
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  106 PHE
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  139 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 145 optimal weight:    8.9990
   chunk 105 optimal weight:    0.6980
   chunk 107 optimal weight:    4.9990
   chunk 128 optimal weight:    3.9990
   chunk 26 optimal weight:    0.2980
   chunk 138 optimal weight:    0.8980
   chunk 144 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 150 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 470 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 143 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.165303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.123487 restraints weight = 27234.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.126327 restraints weight = 14737.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.130120 restraints weight = 9718.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.129718 restraints weight = 8126.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.129552 restraints weight = 7366.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12858  Z= 0.142
  Angle     :  0.641  14.171  17462  Z= 0.309
  Chirality :  0.041   0.186   1943
  Planarity :  0.005   0.053   2286
  Dihedral  :  3.882  19.916   1693
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.91 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.22), residues: 1538
  helix:  1.87 (0.19), residues: 758
  sheet: -0.82 (0.37), residues: 212
  loop : -1.18 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 447 
 TYR   0.023   0.001   TYR B 713 
 PHE   0.028   0.002   PHE D  72 
 TRP   0.013   0.001   TRP B 695 
 HIS   0.005   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (12858)
  covalent geometry    : angle       0.64139 (17462)
  hydrogen bonds       : bond        0.03593 (  618)
  hydrogen bonds       : angle       4.06178 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.8315 (mm) cc_final: 0.8075 (mp)
REVERT: A  337 MET cc_start: 0.6475 (mmm) cc_final: 0.5965 (mmm)
REVERT: A  461 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7319 (tp30)
REVERT: A  652 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7375 (tm-30)
REVERT: B  454 LYS cc_start: 0.8260 (pttm) cc_final: 0.7872 (mmtt)
REVERT: C    8 ASN cc_start: 0.7429 (p0) cc_final: 0.6596 (t0)
REVERT: C  136 GLN cc_start: 0.7405 (tp-100) cc_final: 0.6827 (tp-100)
REVERT: D   23 GLN cc_start: 0.7625 (mp10) cc_final: 0.7168 (mp10)
REVERT: D   29 GLU cc_start: 0.8660 (pt0) cc_final: 0.8269 (mm-30)
REVERT: D   96 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8020 (tt)
REVERT: D  145 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7611 (ttp80)
REVERT: E   66 PRO cc_start: 0.8247 (Cg_exo) cc_final: 0.7996 (Cg_endo)
  outliers start: 25
  outliers final: 18
  residues processed: 171
  average time/residue: 0.0979
  time to fit residues: 26.1051
Evaluate side-chains
  168 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  443 PHE
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  656 THR
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  139 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 108 optimal weight:    0.3980
   chunk 142 optimal weight:    6.9990
   chunk 143 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 115 optimal weight:    0.8980
   chunk 136 optimal weight:    7.9990
   chunk 65 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 470 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  23 GLN
** D   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.165839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.124627 restraints weight = 27273.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.127506 restraints weight = 14253.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.131065 restraints weight = 9430.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.130714 restraints weight = 8374.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.130704 restraints weight = 7369.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.3938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12858  Z= 0.131
  Angle     :  0.646  14.919  17462  Z= 0.308
  Chirality :  0.041   0.216   1943
  Planarity :  0.005   0.053   2286
  Dihedral  :  3.876  18.289   1693
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.56 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.22), residues: 1538
  helix:  1.87 (0.19), residues: 758
  sheet: -0.76 (0.37), residues: 212
  loop : -1.18 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 447 
 TYR   0.022   0.001   TYR B 713 
 PHE   0.026   0.002   PHE A  56 
 TRP   0.015   0.001   TRP E  40 
 HIS   0.004   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12858)
  covalent geometry    : angle       0.64569 (17462)
  hydrogen bonds       : bond        0.03434 (  618)
  hydrogen bonds       : angle       4.04052 ( 1857)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.8284 (mm) cc_final: 0.8048 (mp)
REVERT: A  337 MET cc_start: 0.6401 (mmm) cc_final: 0.5919 (mmm)
REVERT: A  461 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7318 (tp30)
REVERT: A  652 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7369 (tm-30)
REVERT: B  454 LYS cc_start: 0.8242 (pttm) cc_final: 0.7861 (mmtt)
REVERT: C    8 ASN cc_start: 0.7446 (p0) cc_final: 0.6578 (t0)
REVERT: C  136 GLN cc_start: 0.7475 (tp-100) cc_final: 0.6887 (tp-100)
REVERT: D   23 GLN cc_start: 0.7570 (mp10) cc_final: 0.7140 (mp10)
REVERT: D   29 GLU cc_start: 0.8637 (pt0) cc_final: 0.8257 (mm-30)
REVERT: D  111 TYR cc_start: 0.8416 (m-10) cc_final: 0.7913 (m-10)
REVERT: D  145 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7596 (ttp80)
REVERT: E   66 PRO cc_start: 0.8244 (Cg_exo) cc_final: 0.7986 (Cg_endo)
  outliers start: 23
  outliers final: 19
  residues processed: 173
  average time/residue: 0.0941
  time to fit residues: 25.7840
Evaluate side-chains
  168 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  443 PHE
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  656 THR
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue  106 PHE
Chi-restraints excluded: chain E residue  122 LEU
Chi-restraints excluded: chain E residue  139 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 121 optimal weight:    7.9990
   chunk 149 optimal weight:    0.9990
   chunk 132 optimal weight:   20.0000
   chunk 54 optimal weight:    0.9980
   chunk 128 optimal weight:    5.9990
   chunk 111 optimal weight:    0.5980
   chunk 122 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 470 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.165910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.123254 restraints weight = 27232.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.127093 restraints weight = 13985.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.129618 restraints weight = 9602.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.131083 restraints weight = 7767.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.131812 restraints weight = 6899.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12858  Z= 0.132
  Angle     :  0.656  13.507  17462  Z= 0.314
  Chirality :  0.042   0.194   1943
  Planarity :  0.005   0.054   2286
  Dihedral  :  3.870  19.104   1693
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 16.99 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.22), residues: 1538
  helix:  1.88 (0.19), residues: 758
  sheet: -0.69 (0.38), residues: 206
  loop : -1.17 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 447 
 TYR   0.021   0.001   TYR B 713 
 PHE   0.022   0.002   PHE D 106 
 TRP   0.013   0.001   TRP B 695 
 HIS   0.004   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (12858)
  covalent geometry    : angle       0.65553 (17462)
  hydrogen bonds       : bond        0.03464 (  618)
  hydrogen bonds       : angle       4.05233 ( 1857)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2396.60 seconds
wall clock time: 42 minutes 4.38 seconds (2524.38 seconds total)