Starting phenix.real_space_refine
on Wed Jun 11 07:25:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cvc_45959/06_2025/9cvc_45959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cvc_45959/06_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_45959/06_2025/9cvc_45959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cvc_45959/06_2025/9cvc_45959.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cvc_45959/06_2025/9cvc_45959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cvc_45959/06_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.56, per 1000 atoms: 0.76
  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: 3.24
  Conformation dependent library (CDL) restraints added in 1.8 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: 1.32
  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: 4.55

  Time building geometry restraints manager: 3.88 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 198
        2.61 -     3.18: 12177
        3.18 -     3.76: 19210
        3.76 -     4.33: 25517
        4.33 -     4.90: 42820
  Nonbonded interactions: 99922
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 385 "
            pdb=" N   LYS A 386 "
     model   vdw
     2.041 3.120
  nonbonded pdb=" O   SER B 444 "
            pdb=" OG  SER B 445 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" O   PRO D  21 "
            pdb=" OE1 GLN D  23 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" OE2 GLU E  39 "
            pdb=" OG  SER E  59 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" OH  TYR A 648 "
            pdb=" OD2 ASP B 589 "
     model   vdw
     2.146 3.040
  ... (remaining 99917 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 68 or resid 285 through 419 or resid 439 through \ 
 766 or resid 782 through 818))
  selection = (chain 'B' and resid 2 through 818)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.460
  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:             0.020
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     34.370
  Find NCS groups from input model:        0.520
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.520
-------------------------------------------------------------------------------
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  : 1.467 
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: 0.2421
  time to fit residues: 86.9383
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  : 1.298 
-------------------------------------------------------------------------------
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 = 50)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.126919 restraints weight = 26450.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.130572 restraints weight = 13942.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.132990 restraints weight = 9648.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
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  : 1.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7375 (tp30)
REVERT: A  652 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7250 (tm-30)
REVERT: A  751 TRP cc_start: 0.8618 (t60) cc_final: 0.8217 (t60)
REVERT: B   52 PHE cc_start: 0.7331 (t80) cc_final: 0.7113 (t80)
REVERT: C    1 MET cc_start: 0.2722 (mmp) cc_final: 0.2521 (mmt)
REVERT: C   29 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6727 (tm-30)
REVERT: C   74 PHE cc_start: 0.6114 (t80) cc_final: 0.5779 (t80)
REVERT: C  136 GLN cc_start: 0.6736 (tp-100) cc_final: 0.6184 (tp40)
REVERT: D   23 GLN cc_start: 0.7506 (mp10) cc_final: 0.7205 (mp10)
REVERT: D   43 ILE cc_start: 0.5672 (mm) cc_final: 0.5370 (mm)
REVERT: E  113 VAL cc_start: 0.7317 (t) cc_final: 0.7089 (m)
  outliers start: 24
  outliers final: 13
  residues processed: 204
  average time/residue: 0.2319
  time to fit residues: 69.7399
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  : 1.296 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 51 optimal weight:    0.0170
   chunk 22 optimal weight:    0.8980
   chunk 154 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 120 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.8820

-------------------------------------------------------------------------------
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 = 0.4460 r_free = 0.4460 target = 0.166632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.125544 restraints weight = 26720.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.127981 restraints weight = 15307.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.131038 restraints weight = 10407.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12858  Z= 0.148
  Angle     :  0.647  11.775  17462  Z= 0.322
  Chirality :  0.042   0.150   1943
  Planarity :  0.005   0.058   2286
  Dihedral  :  4.004  17.582   1693
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.30 %
    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:  0.49 (0.22), residues: 1538
  helix:  1.90 (0.19), residues: 753
  sheet: -1.14 (0.37), residues: 214
  loop : -1.23 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 751 
 HIS   0.005   0.001   HIS B 724 
 PHE   0.021   0.002   PHE D 106 
 TYR   0.018   0.001   TYR A 648 
 ARG   0.007   0.000   ARG A 667 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  618)
  hydrogen bonds       : angle       4.46539 ( 1857)
  covalent geometry    : bond        0.00346 (12858)
  covalent geometry    : angle       0.64680 (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
  183 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 1.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 MET cc_start: 0.6072 (mmm) cc_final: 0.5698 (mmm)
REVERT: A  461 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7252 (mt-10)
REVERT: A  652 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7147 (tm-30)
REVERT: B   52 PHE cc_start: 0.7398 (t80) cc_final: 0.7112 (t80)
REVERT: C    1 MET cc_start: 0.2837 (mmp) cc_final: 0.2623 (mmm)
REVERT: C   29 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6635 (tm-30)
REVERT: C  136 GLN cc_start: 0.6938 (tp-100) cc_final: 0.6676 (tp40)
REVERT: D   23 GLN cc_start: 0.7558 (mp10) cc_final: 0.7249 (mp10)
REVERT: D   41 LYS cc_start: 0.8734 (tttm) cc_final: 0.8483 (tttm)
REVERT: D   96 LEU cc_start: 0.8415 (pp) cc_final: 0.8014 (tt)
REVERT: D  111 TYR cc_start: 0.8377 (m-10) cc_final: 0.7745 (m-10)
  outliers start: 23
  outliers final: 12
  residues processed: 174
  average time/residue: 0.3543
  time to fit residues: 98.1121
Evaluate side-chains
  157 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 145
  time to evaluate  : 1.862 
-------------------------------------------------------------------------------
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   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:    5.9990
   chunk 8 optimal weight:    0.0570
   chunk 61 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 115 optimal weight:    5.9990
   chunk 150 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 3 optimal weight:   30.0000
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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**
E   7 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.168068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.124979 restraints weight = 26803.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.128967 restraints weight = 13719.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.131605 restraints weight = 9347.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.2768

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= 0.125
  Angle     :  0.609  13.853  17462  Z= 0.301
  Chirality :  0.040   0.150   1943
  Planarity :  0.005   0.055   2286
  Dihedral  :  3.877  18.074   1693
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.31 %
    Favored  : 86.11 %
  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:  0.62 (0.22), residues: 1538
  helix:  1.98 (0.19), residues: 755
  sheet: -0.93 (0.36), residues: 218
  loop : -1.21 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 695 
 HIS   0.004   0.001   HIS B 724 
 PHE   0.019   0.002   PHE D 106 
 TYR   0.024   0.001   TYR A 648 
 ARG   0.009   0.000   ARG A 667 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  618)
  hydrogen bonds       : angle       4.19114 ( 1857)
  covalent geometry    : bond        0.00293 (12858)
  covalent geometry    : angle       0.60893 (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
  186 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 MET cc_start: 0.5997 (mmm) cc_final: 0.5678 (mmm)
REVERT: A  461 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7268 (mt-10)
REVERT: A  652 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7141 (tm-30)
REVERT: B   52 PHE cc_start: 0.7313 (t80) cc_final: 0.7002 (t80)
REVERT: C   29 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6363 (tm-30)
REVERT: D    5 GLN cc_start: 0.8474 (mp10) cc_final: 0.7995 (mp10)
REVERT: D   23 GLN cc_start: 0.7508 (mp10) cc_final: 0.7139 (mp10)
REVERT: D  111 TYR cc_start: 0.8405 (m-10) cc_final: 0.7847 (m-10)
REVERT: D  145 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7383 (ttp80)
REVERT: E   22 PHE cc_start: 0.7353 (m-80) cc_final: 0.6998 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 177
  average time/residue: 0.2023
  time to fit residues: 55.1768
Evaluate side-chains
  161 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
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  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 E residue   14 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0030
   chunk 127 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 139 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    0.7590

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.165776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.123365 restraints weight = 26371.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.126865 restraints weight = 14164.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.129163 restraints weight = 9942.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12858  Z= 0.128
  Angle     :  0.610  13.881  17462  Z= 0.298
  Chirality :  0.040   0.185   1943
  Planarity :  0.005   0.053   2286
  Dihedral  :  3.837  17.863   1693
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.61 %
    Favored  : 84.52 %
  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:  0.69 (0.22), residues: 1538
  helix:  2.06 (0.19), residues: 752
  sheet: -0.78 (0.37), residues: 216
  loop : -1.25 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  40 
 HIS   0.004   0.001   HIS B 724 
 PHE   0.027   0.002   PHE B 443 
 TYR   0.012   0.001   TYR D 117 
 ARG   0.006   0.000   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03597 (  618)
  hydrogen bonds       : angle       4.12367 ( 1857)
  covalent geometry    : bond        0.00303 (12858)
  covalent geometry    : angle       0.61040 (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
  188 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 1.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7785 (mp0)
REVERT: A  317 LEU cc_start: 0.8258 (mm) cc_final: 0.8043 (mp)
REVERT: A  337 MET cc_start: 0.6002 (mmm) cc_final: 0.5776 (mmm)
REVERT: A  461 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7329 (tp30)
REVERT: A  652 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7123 (tm-30)
REVERT: B   52 PHE cc_start: 0.7310 (t80) cc_final: 0.6945 (t80)
REVERT: C    8 ASN cc_start: 0.7329 (p0) cc_final: 0.6664 (t0)
REVERT: C  136 GLN cc_start: 0.7281 (tp-100) cc_final: 0.6741 (tp-100)
REVERT: D   23 GLN cc_start: 0.7566 (mp10) cc_final: 0.7172 (mp10)
REVERT: D   96 LEU cc_start: 0.8440 (pp) cc_final: 0.7973 (tt)
REVERT: D  111 TYR cc_start: 0.8288 (m-10) cc_final: 0.7745 (m-10)
REVERT: D  145 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7416 (ttp80)
REVERT: E   66 PRO cc_start: 0.8093 (Cg_exo) cc_final: 0.7833 (Cg_endo)
  outliers start: 26
  outliers final: 18
  residues processed: 179
  average time/residue: 0.2036
  time to fit residues: 57.2137
Evaluate side-chains
  168 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  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 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  463 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue   26 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 153 optimal weight:    0.7980
   chunk 127 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 138 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 111 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0070
   overall best weight:    0.6798

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.165945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.129134 restraints weight = 26693.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.130711 restraints weight = 14833.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.131057 restraints weight = 10924.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12858  Z= 0.122
  Angle     :  0.600  13.619  17462  Z= 0.293
  Chirality :  0.040   0.178   1943
  Planarity :  0.004   0.054   2286
  Dihedral  :  3.792  17.771   1693
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.76 %
    Favored  : 83.59 %
  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:  0.74 (0.22), residues: 1538
  helix:  2.10 (0.19), residues: 753
  sheet: -0.79 (0.37), residues: 210
  loop : -1.23 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 695 
 HIS   0.004   0.001   HIS B 724 
 PHE   0.033   0.002   PHE B 626 
 TYR   0.013   0.001   TYR C 111 
 ARG   0.005   0.000   ARG D 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03508 (  618)
  hydrogen bonds       : angle       3.99763 ( 1857)
  covalent geometry    : bond        0.00287 (12858)
  covalent geometry    : angle       0.60027 (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
  181 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7753 (mp0)
REVERT: A  317 LEU cc_start: 0.8238 (mm) cc_final: 0.8026 (mp)
REVERT: A  337 MET cc_start: 0.5978 (mmm) cc_final: 0.5764 (mmm)
REVERT: A  461 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7331 (tp30)
REVERT: A  652 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7130 (tm-30)
REVERT: B   52 PHE cc_start: 0.7261 (t80) cc_final: 0.6863 (t80)
REVERT: C    8 ASN cc_start: 0.7297 (p0) cc_final: 0.6584 (t0)
REVERT: C   43 ILE cc_start: 0.7592 (mm) cc_final: 0.7374 (mm)
REVERT: C  136 GLN cc_start: 0.7335 (tp-100) cc_final: 0.6761 (tp40)
REVERT: D   23 GLN cc_start: 0.7626 (mp10) cc_final: 0.7199 (mp10)
REVERT: D   96 LEU cc_start: 0.8100 (pp) cc_final: 0.7700 (tt)
REVERT: D  111 TYR cc_start: 0.7546 (m-10) cc_final: 0.7003 (m-10)
REVERT: D  145 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7490 (ttp80)
REVERT: E   66 PRO cc_start: 0.7907 (Cg_exo) cc_final: 0.7665 (Cg_endo)
  outliers start: 23
  outliers final: 16
  residues processed: 173
  average time/residue: 0.2092
  time to fit residues: 55.3030
Evaluate side-chains
  171 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 155
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
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   15 VAL
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  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain D residue    4 VAL
Chi-restraints excluded: chain D residue   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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 139 optimal weight:    6.9990
   chunk 40 optimal weight:    0.3980
   chunk 86 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 146 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 153 optimal weight:   10.0000
   chunk 143 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.163166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.120159 restraints weight = 26623.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.123606 restraints weight = 14609.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.125829 restraints weight = 10360.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  12858  Z= 0.169
  Angle     :  0.643  13.997  17462  Z= 0.313
  Chirality :  0.042   0.195   1943
  Planarity :  0.005   0.054   2286
  Dihedral  :  3.855  18.123   1693
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.83 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.02 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.60 (0.22), residues: 1538
  helix:  1.88 (0.19), residues: 759
  sheet: -0.83 (0.37), residues: 212
  loop : -1.15 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 475 
 HIS   0.006   0.001   HIS B 724 
 PHE   0.021   0.002   PHE B 505 
 TYR   0.019   0.001   TYR B 713 
 ARG   0.005   0.000   ARG D 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  618)
  hydrogen bonds       : angle       4.04530 ( 1857)
  covalent geometry    : bond        0.00411 (12858)
  covalent geometry    : angle       0.64257 (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
  190 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 1.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7880 (mp0)
REVERT: A  317 LEU cc_start: 0.8331 (mm) cc_final: 0.8098 (mp)
REVERT: A  337 MET cc_start: 0.6031 (mmm) cc_final: 0.5814 (mmm)
REVERT: A  461 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7343 (tp30)
REVERT: A  502 VAL cc_start: 0.6557 (t) cc_final: 0.5135 (m)
REVERT: A  652 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7092 (tm-30)
REVERT: C    8 ASN cc_start: 0.7441 (p0) cc_final: 0.6658 (t0)
REVERT: C  120 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7492 (t)
REVERT: C  136 GLN cc_start: 0.7286 (tp-100) cc_final: 0.6709 (tp-100)
REVERT: D   23 GLN cc_start: 0.7579 (mp10) cc_final: 0.7114 (mp10)
REVERT: D   96 LEU cc_start: 0.8401 (pp) cc_final: 0.8018 (tt)
REVERT: D  145 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7402 (ttp80)
REVERT: E   66 PRO cc_start: 0.8110 (Cg_exo) cc_final: 0.7867 (Cg_endo)
  outliers start: 27
  outliers final: 19
  residues processed: 180
  average time/residue: 0.1999
  time to fit residues: 56.1460
Evaluate side-chains
  174 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
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  692 THR
Chi-restraints excluded: chain B residue   15 VAL
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  502 VAL
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain D residue    4 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 131 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 122 optimal weight:    0.0070
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 109 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.5798

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.165943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.123117 restraints weight = 27142.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.126940 restraints weight = 13800.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.129460 restraints weight = 9453.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12858  Z= 0.124
  Angle     :  0.622  14.564  17462  Z= 0.300
  Chirality :  0.040   0.177   1943
  Planarity :  0.005   0.054   2286
  Dihedral  :  3.831  18.022   1693
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.26 %
    Favored  : 82.94 %
  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:  0.66 (0.22), residues: 1538
  helix:  1.95 (0.19), residues: 759
  sheet: -0.82 (0.37), residues: 212
  loop : -1.15 (0.26), residues: 567

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   0.020   0.002   PHE B 626 
 TYR   0.021   0.001   TYR B 713 
 ARG   0.005   0.000   ARG D 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03535 (  618)
  hydrogen bonds       : angle       4.00446 ( 1857)
  covalent geometry    : bond        0.00289 (12858)
  covalent geometry    : angle       0.62243 (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: 25
    poor density    : 156
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7867 (mp0)
REVERT: A  317 LEU cc_start: 0.8284 (mm) cc_final: 0.8047 (mp)
REVERT: A  337 MET cc_start: 0.5975 (mmm) cc_final: 0.5743 (mmm)
REVERT: A  461 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7342 (tp30)
REVERT: A  652 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7306 (tm-30)
REVERT: C    8 ASN cc_start: 0.7379 (p0) cc_final: 0.6596 (t0)
REVERT: C   37 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7632 (p0)
REVERT: C  136 GLN cc_start: 0.7400 (tp-100) cc_final: 0.7030 (tp-100)
REVERT: D   23 GLN cc_start: 0.7609 (mp10) cc_final: 0.7170 (mp10)
REVERT: D   29 GLU cc_start: 0.8650 (pt0) cc_final: 0.8292 (mm-30)
REVERT: D   96 LEU cc_start: 0.8378 (pp) cc_final: 0.7999 (tt)
REVERT: D  111 TYR cc_start: 0.8358 (m-10) cc_final: 0.7817 (m-10)
  outliers start: 25
  outliers final: 17
  residues processed: 172
  average time/residue: 0.2091
  time to fit residues: 55.5015
Evaluate side-chains
  166 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
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 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  463 LEU
Chi-restraints excluded: chain B residue  656 THR
Chi-restraints excluded: chain B residue  789 VAL
Chi-restraints excluded: chain C residue   23 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue   97 ILE
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
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:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 146 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0870
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.3162

-------------------------------------------------------------------------------
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 498 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.163813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.120257 restraints weight = 27043.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.124025 restraints weight = 14006.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.126484 restraints weight = 9708.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.3840

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= 0.167
  Angle     :  0.659  14.617  17462  Z= 0.320
  Chirality :  0.042   0.195   1943
  Planarity :  0.005   0.061   2286
  Dihedral  :  3.912  20.230   1693
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.84 %
    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:  0.49 (0.22), residues: 1538
  helix:  1.76 (0.19), residues: 759
  sheet: -0.87 (0.37), residues: 212
  loop : -1.18 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E  40 
 HIS   0.006   0.001   HIS B 724 
 PHE   0.037   0.002   PHE A  56 
 TYR   0.023   0.001   TYR B 713 
 ARG   0.006   0.000   ARG D 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  618)
  hydrogen bonds       : angle       4.10658 ( 1857)
  covalent geometry    : bond        0.00404 (12858)
  covalent geometry    : angle       0.65914 (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
  179 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 1.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7873 (mp0)
REVERT: A  337 MET cc_start: 0.6658 (mmm) cc_final: 0.5935 (mmm)
REVERT: A  461 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7343 (tp30)
REVERT: A  502 VAL cc_start: 0.6521 (t) cc_final: 0.5111 (m)
REVERT: A  652 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7369 (tm-30)
REVERT: B  454 LYS cc_start: 0.8259 (pttm) cc_final: 0.7872 (mmtt)
REVERT: C    8 ASN cc_start: 0.7463 (p0) cc_final: 0.6660 (t0)
REVERT: C  136 GLN cc_start: 0.7410 (tp-100) cc_final: 0.6859 (tp-100)
REVERT: D   23 GLN cc_start: 0.7659 (mp10) cc_final: 0.7308 (mp10)
REVERT: D   96 LEU cc_start: 0.8476 (pp) cc_final: 0.8099 (tt)
REVERT: D  111 TYR cc_start: 0.8416 (m-10) cc_final: 0.8001 (m-10)
REVERT: D  145 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7669 (ttp80)
REVERT: E   66 PRO cc_start: 0.8215 (Cg_exo) cc_final: 0.7936 (Cg_endo)
  outliers start: 24
  outliers final: 19
  residues processed: 171
  average time/residue: 0.2142
  time to fit residues: 55.8052
Evaluate side-chains
  169 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  443 PHE
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  692 THR
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  509 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   95 VAL
Chi-restraints excluded: chain C residue   97 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 15 optimal weight:    0.2980
   chunk 140 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0670
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 498 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  20 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.166076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.123518 restraints weight = 26876.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.127397 restraints weight = 13827.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.129925 restraints weight = 9442.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.3933

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= 0.118
  Angle     :  0.638  15.484  17462  Z= 0.304
  Chirality :  0.041   0.255   1943
  Planarity :  0.005   0.058   2286
  Dihedral  :  3.889  19.030   1693
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 16.63 %
    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:  0.64 (0.22), residues: 1538
  helix:  1.94 (0.19), residues: 759
  sheet: -0.84 (0.37), residues: 212
  loop : -1.18 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E  40 
 HIS   0.002   0.001   HIS B 724 
 PHE   0.021   0.001   PHE B 626 
 TYR   0.022   0.001   TYR B 713 
 ARG   0.008   0.000   ARG B 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03380 (  618)
  hydrogen bonds       : angle       4.04348 ( 1857)
  covalent geometry    : bond        0.00278 (12858)
  covalent geometry    : angle       0.63776 (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
  170 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7882 (mp0)
REVERT: A  337 MET cc_start: 0.6621 (mmm) cc_final: 0.5900 (mmm)
REVERT: A  461 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7345 (tp30)
REVERT: A  652 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7364 (tm-30)
REVERT: B  454 LYS cc_start: 0.8254 (pttm) cc_final: 0.7898 (mmtt)
REVERT: C    8 ASN cc_start: 0.7393 (p0) cc_final: 0.6556 (t0)
REVERT: C   43 ILE cc_start: 0.7449 (mm) cc_final: 0.7193 (mm)
REVERT: C  136 GLN cc_start: 0.7422 (tp-100) cc_final: 0.7028 (tp-100)
REVERT: D   23 GLN cc_start: 0.7775 (mp10) cc_final: 0.7272 (mp10)
REVERT: D   96 LEU cc_start: 0.8433 (pp) cc_final: 0.7986 (tt)
REVERT: D  111 TYR cc_start: 0.8326 (m-10) cc_final: 0.7830 (m-10)
REVERT: D  145 ARG cc_start: 0.8060 (ttm170) cc_final: 0.7612 (ttp80)
REVERT: E   66 PRO cc_start: 0.8170 (Cg_exo) cc_final: 0.7894 (Cg_endo)
  outliers start: 13
  outliers final: 12
  residues processed: 166
  average time/residue: 0.2157
  time to fit residues: 55.5340
Evaluate side-chains
  163 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
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  701 SER
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   95 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  139 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 71 optimal weight:    0.0870
   chunk 15 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0570
   chunk 113 optimal weight:    2.9990
   chunk 140 optimal weight:    8.9990
   overall best weight:    0.5676

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.165946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.123408 restraints weight = 26894.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.127349 restraints weight = 13777.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.129883 restraints weight = 9402.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.4018

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= 0.120
  Angle     :  0.635  15.339  17462  Z= 0.302
  Chirality :  0.041   0.278   1943
  Planarity :  0.005   0.057   2286
  Dihedral  :  3.846  19.161   1693
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.20 %
    Favored  : 82.51 %
  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:  0.71 (0.22), residues: 1538
  helix:  2.01 (0.19), residues: 760
  sheet: -0.70 (0.37), residues: 206
  loop : -1.20 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E  40 
 HIS   0.004   0.001   HIS A 450 
 PHE   0.020   0.001   PHE A  56 
 TYR   0.021   0.001   TYR B 713 
 ARG   0.008   0.000   ARG B 447 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03348 (  618)
  hydrogen bonds       : angle       3.97402 ( 1857)
  covalent geometry    : bond        0.00284 (12858)
  covalent geometry    : angle       0.63457 (17462)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4855.20 seconds
wall clock time: 85 minutes 23.59 seconds (5123.59 seconds total)