Starting phenix.real_space_refine
on Thu May 15 02:01:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cvc_45959/05_2025/9cvc_45959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cvc_45959/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cvc_45959/05_2025/9cvc_45959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cvc_45959/05_2025/9cvc_45959.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cvc_45959/05_2025/9cvc_45959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cvc_45959/05_2025/9cvc_45959.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.014
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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.07, per 1000 atoms: 0.72
  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: 3.04
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.26
  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: 3.53

  Time building geometry restraints manager: 3.60 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:                  0.010
  Normalize map: mean=0, sd=1:             15.130
  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:             0.030
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.460
  Process input model:                     31.580
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.240
-------------------------------------------------------------------------------
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 : 14.29
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (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
 TRP   0.017   0.002   TRP B  21 
 HIS   0.007   0.001   HIS B 470 
 PHE   0.023   0.002   PHE B 443 
 TYR   0.030   0.002   TYR C 111 
 ARG   0.020   0.001   ARG A  58 

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

*********************** 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  : 1.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7040 (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: 0.7755 (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: 0.2339
  time to fit residues: 83.2948
Evaluate side-chains
  172 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    7.9990
   chunk 117 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0870
   chunk 79 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 121 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9990
   chunk 90 optimal weight:    0.5980
   chunk 140 optimal weight:    9.9990
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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
** 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.168957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.126868 restraints weight = 26450.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.130555 restraints weight = 13959.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.132996 restraints weight = 9652.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.1884

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= 0.156
  Angle     :  0.697  10.196  17462  Z= 0.355
  Chirality :  0.043   0.174   1943
  Planarity :  0.005   0.068   2286
  Dihedral  :  4.060  17.992   1693
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  8.71 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.22), residues: 1538
  helix:  1.75 (0.19), residues: 746
  sheet: -1.06 (0.39), residues: 195
  loop : -1.18 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E  40 
 HIS   0.004   0.001   HIS B 724 
 PHE   0.030   0.002   PHE D 106 
 TYR   0.016   0.002   TYR A 648 
 ARG   0.004   0.001   ARG C 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04536 (  618)
  hydrogen bonds       : angle       4.67326 ( 1857)
  covalent geometry    : bond        0.00350 (12858)
  covalent geometry    : angle       0.69686 (17462)

*********************** 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
  217 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 193
  time to evaluate  : 1.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7384 (tp30)
REVERT: A  652 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7255 (tm-30)
REVERT: A  751 TRP cc_start: 0.8620 (t60) cc_final: 0.8222 (t60)
REVERT: B   52 PHE cc_start: 0.7336 (t80) cc_final: 0.7117 (t80)
REVERT: C    1 MET cc_start: 0.2720 (mmp) cc_final: 0.2516 (mmt)
REVERT: C   29 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6720 (tm-30)
REVERT: C   74 PHE cc_start: 0.6099 (t80) cc_final: 0.5764 (t80)
REVERT: C  136 GLN cc_start: 0.6740 (tp-100) cc_final: 0.6187 (tp40)
REVERT: D   23 GLN cc_start: 0.7501 (mp10) cc_final: 0.7202 (mp10)
REVERT: D   43 ILE cc_start: 0.5673 (mm) cc_final: 0.5371 (mm)
REVERT: E  113 VAL cc_start: 0.7323 (t) cc_final: 0.7094 (m)
  outliers start: 24
  outliers final: 13
  residues processed: 204
  average time/residue: 0.2410
  time to fit residues: 72.8081
Evaluate side-chains
  165 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
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   23 GLN
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 50 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0970
   chunk 22 optimal weight:    0.6980
   chunk 154 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 120 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  55 GLN
** D   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.166502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.125312 restraints weight = 26720.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.127459 restraints weight = 16113.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.129665 restraints weight = 10794.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12858  Z= 0.147
  Angle     :  0.646  11.564  17462  Z= 0.321
  Chirality :  0.042   0.158   1943
  Planarity :  0.005   0.059   2286
  Dihedral  :  4.011  17.615   1693
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.37 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.22), residues: 1538
  helix:  1.88 (0.19), residues: 754
  sheet: -1.14 (0.37), residues: 214
  loop : -1.26 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 751 
 HIS   0.005   0.001   HIS B 724 
 PHE   0.021   0.002   PHE A 477 
 TYR   0.018   0.001   TYR A 648 
 ARG   0.007   0.000   ARG A 667 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  618)
  hydrogen bonds       : angle       4.44427 ( 1857)
  covalent geometry    : bond        0.00351 (12858)
  covalent geometry    : angle       0.64560 (17462)

*********************** 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
  186 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 1.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 MET cc_start: 0.6091 (mmm) cc_final: 0.5712 (mmm)
REVERT: A  461 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7282 (mt-10)
REVERT: A  652 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7151 (tm-30)
REVERT: B   52 PHE cc_start: 0.7375 (t80) cc_final: 0.7085 (t80)
REVERT: C    1 MET cc_start: 0.2908 (mmp) cc_final: 0.2646 (mmm)
REVERT: C   29 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6370 (tm-30)
REVERT: C  136 GLN cc_start: 0.7028 (tp-100) cc_final: 0.6761 (tp40)
REVERT: D   23 GLN cc_start: 0.7567 (mp10) cc_final: 0.7239 (mp10)
REVERT: D   41 LYS cc_start: 0.8749 (tttm) cc_final: 0.8511 (tttm)
REVERT: D   96 LEU cc_start: 0.8413 (pp) cc_final: 0.8019 (tt)
REVERT: D  111 TYR cc_start: 0.8324 (m-10) cc_final: 0.7692 (m-10)
  outliers start: 22
  outliers final: 13
  residues processed: 176
  average time/residue: 0.2281
  time to fit residues: 62.1427
Evaluate side-chains
  161 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
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  701 SER
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   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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 149 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 76 optimal weight:    0.6980
   chunk 115 optimal weight:    5.9990
   chunk 150 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 3 optimal weight:   30.0000
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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**
B 553 GLN
** 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 = 0.4437 r_free = 0.4437 target = 0.164789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.123669 restraints weight = 26443.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.125831 restraints weight = 14887.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.127660 restraints weight = 10388.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12858  Z= 0.152
  Angle     :  0.627  13.306  17462  Z= 0.312
  Chirality :  0.041   0.154   1943
  Planarity :  0.005   0.056   2286
  Dihedral  :  3.925  18.500   1693
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.60 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.22), residues: 1538
  helix:  1.86 (0.19), residues: 757
  sheet: -0.89 (0.36), residues: 214
  loop : -1.18 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 695 
 HIS   0.005   0.001   HIS B 724 
 PHE   0.028   0.002   PHE B 443 
 TYR   0.026   0.002   TYR A 648 
 ARG   0.014   0.001   ARG A 667 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03857 (  618)
  hydrogen bonds       : angle       4.21989 ( 1857)
  covalent geometry    : bond        0.00365 (12858)
  covalent geometry    : angle       0.62658 (17462)

*********************** 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
  192 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 1.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 MET cc_start: 0.6034 (mmm) cc_final: 0.5713 (mmm)
REVERT: A  461 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7278 (mt-10)
REVERT: A  652 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7167 (tm-30)
REVERT: B   52 PHE cc_start: 0.7367 (t80) cc_final: 0.7019 (t80)
REVERT: C    1 MET cc_start: 0.3103 (mmp) cc_final: 0.2882 (mmm)
REVERT: C   29 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6271 (tm-30)
REVERT: D    5 GLN cc_start: 0.8438 (mp10) cc_final: 0.7945 (mp10)
REVERT: D   23 GLN cc_start: 0.7542 (mp10) cc_final: 0.7155 (mp10)
REVERT: D   41 LYS cc_start: 0.8770 (tttm) cc_final: 0.8393 (tttm)
REVERT: D   96 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8038 (tt)
REVERT: D  111 TYR cc_start: 0.8231 (m-10) cc_final: 0.7869 (m-10)
REVERT: D  145 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7415 (ttp80)
  outliers start: 28
  outliers final: 14
  residues processed: 183
  average time/residue: 0.2138
  time to fit residues: 59.9609
Evaluate side-chains
  164 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
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   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    4 VAL
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue   96 LEU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue  122 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 105 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   chunk 127 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 139 optimal weight:    2.9990
   chunk 108 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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 498 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 143 ASN
E   7 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.163242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.121907 restraints weight = 26508.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.124154 restraints weight = 14799.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.125898 restraints weight = 10384.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
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   0.059  12858  Z= 0.166
  Angle     :  0.639  13.078  17462  Z= 0.315
  Chirality :  0.041   0.196   1943
  Planarity :  0.005   0.053   2286
  Dihedral  :  3.947  17.780   1693
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.69 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.22), residues: 1538
  helix:  1.80 (0.19), residues: 757
  sheet: -0.88 (0.37), residues: 217
  loop : -1.19 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  40 
 HIS   0.006   0.001   HIS B 724 
 PHE   0.023   0.002   PHE B 443 
 TYR   0.018   0.001   TYR B 713 
 ARG   0.005   0.000   ARG D 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  618)
  hydrogen bonds       : angle       4.17706 ( 1857)
  covalent geometry    : bond        0.00397 (12858)
  covalent geometry    : angle       0.63895 (17462)

*********************** 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
  189 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 1.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7839 (mp0)
REVERT: A  317 LEU cc_start: 0.8373 (mm) cc_final: 0.8109 (mp)
REVERT: A  337 MET cc_start: 0.6035 (mmm) cc_final: 0.5739 (mmm)
REVERT: A  461 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7389 (tp30)
REVERT: A  502 VAL cc_start: 0.6520 (t) cc_final: 0.5113 (m)
REVERT: A  652 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7155 (tm-30)
REVERT: C    1 MET cc_start: 0.3145 (mmp) cc_final: 0.2936 (mmm)
REVERT: C   29 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6227 (tm-30)
REVERT: C  136 GLN cc_start: 0.7156 (tp40) cc_final: 0.6305 (tp-100)
REVERT: D   23 GLN cc_start: 0.7607 (mp10) cc_final: 0.7211 (mp10)
REVERT: D   29 GLU cc_start: 0.8663 (pt0) cc_final: 0.8343 (mm-30)
REVERT: D   96 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7949 (tt)
REVERT: D  111 TYR cc_start: 0.8382 (m-10) cc_final: 0.7894 (m-10)
REVERT: D  145 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7435 (ttp80)
  outliers start: 31
  outliers final: 22
  residues processed: 177
  average time/residue: 0.1987
  time to fit residues: 54.7138
Evaluate side-chains
  171 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 1.399 
-------------------------------------------------------------------------------
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  443 PHE
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 A residue  701 SER
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  463 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  502 VAL
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   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  139 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 135 optimal weight:    0.0050
   chunk 153 optimal weight:    6.9990
   chunk 127 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0170
   chunk 138 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 124 optimal weight:    0.0170
   chunk 111 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.3070

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

Flipped N/Q/H residues before XYZ refinement:
A 406 GLN
A 553 GLN
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 498 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 143 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.165459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.122828 restraints weight = 26756.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.126357 restraints weight = 14295.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.128654 restraints weight = 10015.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.3429

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= 0.116
  Angle     :  0.613  14.519  17462  Z= 0.296
  Chirality :  0.040   0.179   1943
  Planarity :  0.005   0.055   2286
  Dihedral  :  3.886  19.713   1693
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.83 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.22), residues: 1538
  helix:  1.97 (0.19), residues: 757
  sheet: -0.64 (0.38), residues: 198
  loop : -1.17 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 695 
 HIS   0.002   0.001   HIS B 724 
 PHE   0.014   0.001   PHE A 477 
 TYR   0.032   0.001   TYR D 101 
 ARG   0.005   0.000   ARG D 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  618)
  hydrogen bonds       : angle       4.04122 ( 1857)
  covalent geometry    : bond        0.00262 (12858)
  covalent geometry    : angle       0.61333 (17462)

*********************** 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
  195 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 1.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7826 (mp0)
REVERT: A  317 LEU cc_start: 0.8302 (mm) cc_final: 0.8067 (mp)
REVERT: A  337 MET cc_start: 0.6038 (mmm) cc_final: 0.5810 (mmm)
REVERT: A  461 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7327 (tp30)
REVERT: A  652 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7242 (tm-30)
REVERT: B  454 LYS cc_start: 0.8222 (pttm) cc_final: 0.7925 (mmtt)
REVERT: C    8 ASN cc_start: 0.7203 (p0) cc_final: 0.6560 (t0)
REVERT: C   29 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6405 (tm-30)
REVERT: C   31 ILE cc_start: 0.8291 (mp) cc_final: 0.7886 (mm)
REVERT: D   23 GLN cc_start: 0.7570 (mp10) cc_final: 0.7133 (mp10)
REVERT: D   96 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7860 (tt)
REVERT: D  111 TYR cc_start: 0.8362 (m-10) cc_final: 0.7798 (m-10)
REVERT: D  145 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7368 (ttp80)
  outliers start: 30
  outliers final: 14
  residues processed: 185
  average time/residue: 0.2108
  time to fit residues: 58.8329
Evaluate side-chains
  166 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
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 B residue  304 LEU
Chi-restraints excluded: chain B residue  656 THR
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 139 optimal weight:    6.9990
   chunk 40 optimal weight:    0.1980
   chunk 86 optimal weight:    0.0470
   chunk 81 optimal weight:    0.6980
   chunk 146 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 153 optimal weight:    0.5980
   chunk 143 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 470 HIS
** B 508 GLN ** 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 = 0.4466 r_free = 0.4466 target = 0.166989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.125630 restraints weight = 27084.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.128456 restraints weight = 14591.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.132460 restraints weight = 9678.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.3587

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= 0.114
  Angle     :  0.604  12.589  17462  Z= 0.291
  Chirality :  0.040   0.167   1943
  Planarity :  0.005   0.055   2286
  Dihedral  :  3.822  20.260   1693
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.05 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.22), residues: 1538
  helix:  2.02 (0.19), residues: 760
  sheet: -0.66 (0.38), residues: 198
  loop : -1.12 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 695 
 HIS   0.003   0.000   HIS B 724 
 PHE   0.039   0.001   PHE B 626 
 TYR   0.018   0.001   TYR B 713 
 ARG   0.009   0.000   ARG B 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03391 (  618)
  hydrogen bonds       : angle       3.97498 ( 1857)
  covalent geometry    : bond        0.00264 (12858)
  covalent geometry    : angle       0.60368 (17462)

*********************** 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
  185 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7885 (mp0)
REVERT: A  317 LEU cc_start: 0.8297 (mm) cc_final: 0.8061 (mp)
REVERT: A  337 MET cc_start: 0.5885 (mmm) cc_final: 0.5661 (mmm)
REVERT: A  461 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7308 (tp30)
REVERT: A  652 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7294 (tm-30)
REVERT: B  454 LYS cc_start: 0.8263 (pttm) cc_final: 0.8002 (mmtt)
REVERT: B  550 MET cc_start: 0.5504 (mpp) cc_final: 0.5016 (mpp)
REVERT: C    8 ASN cc_start: 0.7333 (p0) cc_final: 0.6552 (t0)
REVERT: C   29 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6286 (tm-30)
REVERT: C   31 ILE cc_start: 0.8193 (mp) cc_final: 0.7782 (mm)
REVERT: D   23 GLN cc_start: 0.7592 (mp10) cc_final: 0.7146 (mp10)
REVERT: D  111 TYR cc_start: 0.8416 (m-10) cc_final: 0.7864 (m-10)
REVERT: E   66 PRO cc_start: 0.8262 (Cg_exo) cc_final: 0.7988 (Cg_endo)
  outliers start: 27
  outliers final: 16
  residues processed: 176
  average time/residue: 0.2140
  time to fit residues: 57.5703
Evaluate side-chains
  166 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 LEU
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 B residue  304 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  656 THR
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue  106 PHE
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  139 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 131 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 122 optimal weight:    0.1980
   chunk 48 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 109 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 470 HIS
** B 508 GLN ** 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 = 0.4462 r_free = 0.4462 target = 0.166724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.125164 restraints weight = 27172.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.128096 restraints weight = 14837.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.131767 restraints weight = 9800.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12858  Z= 0.117
  Angle     :  0.608  13.368  17462  Z= 0.292
  Chirality :  0.040   0.171   1943
  Planarity :  0.004   0.056   2286
  Dihedral  :  3.772  18.886   1693
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.62 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.22), residues: 1538
  helix:  2.02 (0.19), residues: 759
  sheet: -0.68 (0.38), residues: 198
  loop : -1.13 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 695 
 HIS   0.003   0.001   HIS B 724 
 PHE   0.022   0.001   PHE B 626 
 TYR   0.016   0.001   TYR B 713 
 ARG   0.006   0.000   ARG B 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03345 (  618)
  hydrogen bonds       : angle       3.97196 ( 1857)
  covalent geometry    : bond        0.00275 (12858)
  covalent geometry    : angle       0.60812 (17462)

*********************** 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
  181 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7911 (mp0)
REVERT: A  317 LEU cc_start: 0.8274 (mm) cc_final: 0.8043 (mp)
REVERT: A  337 MET cc_start: 0.6274 (mmm) cc_final: 0.5938 (mmm)
REVERT: A  461 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7323 (tp30)
REVERT: A  489 MET cc_start: 0.8206 (tpp) cc_final: 0.8002 (tpp)
REVERT: A  652 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7333 (tm-30)
REVERT: B  550 MET cc_start: 0.5615 (mpp) cc_final: 0.5151 (mpp)
REVERT: C    8 ASN cc_start: 0.7343 (p0) cc_final: 0.6517 (t0)
REVERT: C   31 ILE cc_start: 0.8229 (mp) cc_final: 0.7965 (mm)
REVERT: C  136 GLN cc_start: 0.7096 (tp-100) cc_final: 0.6567 (tp-100)
REVERT: D   23 GLN cc_start: 0.7591 (mp10) cc_final: 0.7156 (mp10)
REVERT: D   96 LEU cc_start: 0.8419 (pp) cc_final: 0.7971 (tt)
REVERT: D  111 TYR cc_start: 0.8514 (m-10) cc_final: 0.7998 (m-10)
REVERT: D  145 ARG cc_start: 0.7974 (ttm170) cc_final: 0.7540 (ttp80)
REVERT: E   66 PRO cc_start: 0.8261 (Cg_exo) cc_final: 0.8000 (Cg_endo)
  outliers start: 22
  outliers final: 15
  residues processed: 174
  average time/residue: 0.2017
  time to fit residues: 54.4062
Evaluate side-chains
  165 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
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  304 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   90 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue   30 CYS
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  139 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 138 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 84 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 146 optimal weight:    0.1980
   chunk 73 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 470 HIS
** B 508 GLN ** 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 = 0.4460 r_free = 0.4460 target = 0.166409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.123485 restraints weight = 27002.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.127401 restraints weight = 13949.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.129933 restraints weight = 9596.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12858  Z= 0.122
  Angle     :  0.618  13.302  17462  Z= 0.296
  Chirality :  0.041   0.184   1943
  Planarity :  0.004   0.055   2286
  Dihedral  :  3.756  19.282   1693
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.05 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.22), residues: 1538
  helix:  2.03 (0.19), residues: 759
  sheet: -0.61 (0.38), residues: 198
  loop : -1.13 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 695 
 HIS   0.004   0.001   HIS B 724 
 PHE   0.023   0.002   PHE B 626 
 TYR   0.017   0.001   TYR B 713 
 ARG   0.009   0.000   ARG B 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03342 (  618)
  hydrogen bonds       : angle       3.94856 ( 1857)
  covalent geometry    : bond        0.00292 (12858)
  covalent geometry    : angle       0.61841 (17462)

*********************** 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
  175 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7885 (mp0)
REVERT: A  317 LEU cc_start: 0.8275 (mm) cc_final: 0.8064 (mp)
REVERT: A  337 MET cc_start: 0.6415 (mmm) cc_final: 0.6082 (mmm)
REVERT: A  461 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7328 (tp30)
REVERT: A  489 MET cc_start: 0.8272 (tpp) cc_final: 0.8035 (tpp)
REVERT: A  652 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7380 (tm-30)
REVERT: B  454 LYS cc_start: 0.8191 (pttm) cc_final: 0.7972 (mmtt)
REVERT: B  550 MET cc_start: 0.5796 (mpp) cc_final: 0.5308 (mpp)
REVERT: C    8 ASN cc_start: 0.7395 (p0) cc_final: 0.6533 (t0)
REVERT: C   31 ILE cc_start: 0.8266 (mp) cc_final: 0.7994 (mm)
REVERT: C  136 GLN cc_start: 0.7137 (tp-100) cc_final: 0.6580 (tp-100)
REVERT: D   23 GLN cc_start: 0.7645 (mp10) cc_final: 0.7277 (mp10)
REVERT: D   96 LEU cc_start: 0.8320 (pp) cc_final: 0.7921 (tt)
REVERT: D  111 TYR cc_start: 0.8419 (m-10) cc_final: 0.7896 (m-10)
REVERT: D  145 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7580 (ttp80)
REVERT: E   66 PRO cc_start: 0.8108 (Cg_exo) cc_final: 0.7840 (Cg_endo)
  outliers start: 18
  outliers final: 15
  residues processed: 168
  average time/residue: 0.2141
  time to fit residues: 55.3500
Evaluate side-chains
  165 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASN
Chi-restraints excluded: chain A residue  208 LEU
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 B residue  304 LEU
Chi-restraints excluded: chain B residue  375 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   90 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain E residue   14 ASN
Chi-restraints excluded: chain E residue  106 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 140 optimal weight:    0.1980
   chunk 17 optimal weight:    0.0770
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 78 optimal weight:    0.4980
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 470 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  23 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 = 0.4465 r_free = 0.4465 target = 0.166838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.124417 restraints weight = 26916.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.128311 restraints weight = 13738.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.130844 restraints weight = 9413.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12858  Z= 0.117
  Angle     :  0.620  13.958  17462  Z= 0.296
  Chirality :  0.040   0.244   1943
  Planarity :  0.005   0.055   2286
  Dihedral  :  3.743  18.768   1693
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.13 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.22), residues: 1538
  helix:  2.01 (0.19), residues: 764
  sheet: -0.53 (0.39), residues: 198
  loop : -1.16 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 695 
 HIS   0.003   0.001   HIS B 724 
 PHE   0.023   0.001   PHE A 477 
 TYR   0.018   0.001   TYR B 713 
 ARG   0.008   0.000   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03285 (  618)
  hydrogen bonds       : angle       3.92788 ( 1857)
  covalent geometry    : bond        0.00277 (12858)
  covalent geometry    : angle       0.61972 (17462)

********************** 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
  176 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7874 (mp0)
REVERT: A  337 MET cc_start: 0.6537 (mmm) cc_final: 0.5850 (mmm)
REVERT: A  401 PHE cc_start: 0.5084 (m-80) cc_final: 0.4883 (m-80)
REVERT: A  461 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7306 (tp30)
REVERT: A  489 MET cc_start: 0.8230 (tpp) cc_final: 0.8003 (tpp)
REVERT: A  652 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7383 (tm-30)
REVERT: B  454 LYS cc_start: 0.8227 (pttm) cc_final: 0.7994 (mmtt)
REVERT: B  550 MET cc_start: 0.5735 (mpp) cc_final: 0.5238 (mpp)
REVERT: C    8 ASN cc_start: 0.7368 (p0) cc_final: 0.6501 (t0)
REVERT: C  136 GLN cc_start: 0.7142 (tp-100) cc_final: 0.6558 (tp-100)
REVERT: D   23 GLN cc_start: 0.7810 (mp10) cc_final: 0.7266 (mp10)
REVERT: D   96 LEU cc_start: 0.8270 (pp) cc_final: 0.7920 (tt)
REVERT: D  111 TYR cc_start: 0.8343 (m-10) cc_final: 0.7899 (m-10)
REVERT: D  145 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7599 (ttp80)
REVERT: E   66 PRO cc_start: 0.8084 (Cg_exo) cc_final: 0.7809 (Cg_endo)
  outliers start: 20
  outliers final: 14
  residues processed: 168
  average time/residue: 0.2102
  time to fit residues: 54.8885
Evaluate side-chains
  161 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 LEU
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 B residue  304 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   90 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue   30 CYS
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain E residue  106 PHE
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 71 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 108 optimal weight:    0.4980
   chunk 53 optimal weight:    0.0980
   chunk 26 optimal weight:    0.4980
   chunk 24 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 140 optimal weight:    0.5980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 470 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  20 ASN
** D  23 GLN ** 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 = 0.4465 r_free = 0.4465 target = 0.167116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.124878 restraints weight = 27085.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.128821 restraints weight = 13863.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.131395 restraints weight = 9480.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12858  Z= 0.115
  Angle     :  0.627  12.557  17462  Z= 0.297
  Chirality :  0.041   0.256   1943
  Planarity :  0.005   0.055   2286
  Dihedral  :  3.715  18.319   1693
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 16.56 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.22), residues: 1538
  helix:  1.99 (0.19), residues: 765
  sheet: -0.47 (0.39), residues: 201
  loop : -1.13 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 695 
 HIS   0.003   0.001   HIS B 724 
 PHE   0.038   0.002   PHE A  56 
 TYR   0.017   0.001   TYR B 713 
 ARG   0.009   0.000   ARG B 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03278 (  618)
  hydrogen bonds       : angle       3.92711 ( 1857)
  covalent geometry    : bond        0.00271 (12858)
  covalent geometry    : angle       0.62661 (17462)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4544.64 seconds
wall clock time: 81 minutes 58.24 seconds (4918.24 seconds total)