Starting phenix.real_space_refine
on Sat May 10 07:15:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mnx_48442/05_2025/9mnx_48442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mnx_48442/05_2025/9mnx_48442.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mnx_48442/05_2025/9mnx_48442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mnx_48442/05_2025/9mnx_48442.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mnx_48442/05_2025/9mnx_48442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mnx_48442/05_2025/9mnx_48442.cif"
  }
  resolution = 3.11
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 379 atoms to isotropic.
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      29      5.16       5
     C    3332      2.51       5
     N     909      2.21       5
     O     970      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5240
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 961
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 7, 'TRANS': 112}
    Chain: "A"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 823
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 4, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 962
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
    Chain: "E"
      Number of atoms: 850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 850
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "C"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 950
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
    Chain: "F"
      Number of atoms: 672
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 669
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 85, 669
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 672
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'I2R': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.79, per 1000 atoms: 0.72
  Number of scatterers: 5240
  At special positions: 0
  Unit cell: (94.6, 72.24, 148.78, 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      29     16.00
     O     970      8.00
     N     909      7.00
     C    3332      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.06
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 594.1 milliseconds
  

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1222

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 10 sheets defined
      37.1% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 24
      removed outlier: 3.597A  pdb=" N   ARG B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU B  17 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 33
    Processing helix  chain 'B' and resid 43 through 60
      removed outlier: 4.007A  pdb=" N   ILE B  47 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LEU B  52 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   VAL B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   CYS B  54 " --> pdb=" O   TRP B  50 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ALA B  55 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 89
      removed outlier: 3.659A  pdb=" N   SER B  72 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   ARG B  84 " --> pdb=" O   PHE B  80 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   TYR B  85 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER B  86 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 121
      removed outlier: 3.671A  pdb=" N   ARG B 116 " --> pdb=" O   PHE B 112 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   TYR B 117 " --> pdb=" O   ARG B 113 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASN B 118 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLN B 119 " --> pdb=" O   TRP B 115 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU B 120 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 22
    Processing helix  chain 'A' and resid 24 through 29
      removed outlier: 3.585A  pdb=" N   TRP A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 43
      removed outlier: 4.121A  pdb=" N   ASN A  33 " --> pdb=" O   GLY A  29 " (cutoff:3.500A)
      Proline residue:  A  37  - end of helix
    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 52 through 72
      removed outlier: 3.666A  pdb=" N   CYS A  61 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   LEU A  64 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   MET A  67 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ARG A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A  70 " --> pdb=" O   PHE A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 107
      removed outlier: 3.854A  pdb=" N   VAL A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LEU A  98 " --> pdb=" O   GLN A  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 77
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.873A  pdb=" N   THR C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 374 through 382
      removed outlier: 4.050A  pdb=" N   GLY F 380 " --> pdb=" O   GLU F 376 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE F 382 " --> pdb=" O   ARG F 378 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 394 through 400
    Processing helix  chain 'F' and resid 400 through 406
      removed outlier: 3.665A  pdb=" N   GLU F 404 " --> pdb=" O   LYS F 400 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   HIS F 405 " --> pdb=" O   LYS F 401 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 421 through 429
      removed outlier: 3.512A  pdb=" N   TYR F 425 " --> pdb=" O   GLN F 421 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLU F 426 " --> pdb=" O   SER F 422 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASN F 429 " --> pdb=" O   TYR F 425 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 434 through 448
      removed outlier: 3.590A  pdb=" N   ARG F 438 " --> pdb=" O   ASN F 434 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ASN F 439 " --> pdb=" O   GLU F 435 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLY F 440 " --> pdb=" O   ALA F 436 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN F 443 " --> pdb=" O   ASN F 439 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 451 through 467
      removed outlier: 3.682A  pdb=" N   LYS F 461 " --> pdb=" O   GLY F 457 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER F 465 " --> pdb=" O   LYS F 461 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7
      removed outlier: 3.506A  pdb=" N   LEU D  81 " --> pdb=" O   LEU D  20 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   SER D  71 " --> pdb=" O   TYR D  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 60
      removed outlier: 6.586A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLY D  33 " --> pdb=" O   ARG D  99 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG D  99 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR D 117 " --> pdb=" O   TYR D  94 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 5 through 6
    Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 6
      removed outlier: 3.518A  pdb=" N   ASP E  76 " --> pdb=" O   SER E  73 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 11
      removed outlier: 3.633A  pdb=" N   TYR E  92 " --> pdb=" O   THR E 107 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR E  93 " --> pdb=" O   TYR E  42 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU E  39 " --> pdb=" O   TYR E  55 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   TYR E  55 " --> pdb=" O   LEU E  39 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   TRP E  41 " --> pdb=" O   LEU E  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 11
      removed outlier: 3.633A  pdb=" N   TYR E  92 " --> pdb=" O   THR E 107 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR E 102 " --> pdb=" O   GLN E  96 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 30 through 31
      removed outlier: 3.697A  pdb=" N   LYS E  36 " --> pdb=" O   TYR E  31 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 7
      removed outlier: 3.603A  pdb=" N   SER C   7 " --> pdb=" O   SER C  21 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER C  70 " --> pdb=" O   TYR C  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 13
      removed outlier: 3.546A  pdb=" N   ALA C  96 " --> pdb=" O   GLY C  35 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ARG C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   LEU C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER C  50 " --> pdb=" O   ASN C  58 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 13

    231 hydrogen bonds defined for protein.
    615 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: 1.23

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1000
        1.32 -     1.45: 1661
        1.45 -     1.58: 2658
        1.58 -     1.71: 0
        1.71 -     1.84: 48
  Bond restraints: 5367
  Sorted by residual:
  bond pdb=" C22 I2R A 201 "
       pdb=" N4  I2R A 201 "
    ideal  model  delta    sigma   weight residual
    1.156  1.371 -0.215 2.00e-02 2.50e+03 1.15e+02
  bond pdb=" C   SER B  95 "
       pdb=" O   SER B  95 "
    ideal  model  delta    sigma   weight residual
    1.236  1.315 -0.079 1.18e-02 7.18e+03 4.46e+01
  bond pdb=" C9  I2R A 201 "
       pdb=" N3  I2R A 201 "
    ideal  model  delta    sigma   weight residual
    1.413  1.299  0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" C   ALA B  98 "
       pdb=" O   ALA B  98 "
    ideal  model  delta    sigma   weight residual
    1.236  1.293 -0.057 1.16e-02 7.43e+03 2.38e+01
  bond pdb=" C   PHE B  97 "
       pdb=" O   PHE B  97 "
    ideal  model  delta    sigma   weight residual
    1.236  1.290 -0.054 1.15e-02 7.56e+03 2.21e+01
  ... (remaining 5362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.18: 6917
        3.18 -     6.36: 318
        6.36 -     9.54: 25
        9.54 -    12.72: 4
       12.72 -    15.90: 1
  Bond angle restraints: 7265
  Sorted by residual:
  angle pdb=" N   ASP B  18 "
        pdb=" CA  ASP B  18 "
        pdb=" C   ASP B  18 "
      ideal   model   delta    sigma   weight residual
     111.36  103.26    8.10 1.09e+00 8.42e-01 5.52e+01
  angle pdb=" N   PRO B  91 "
        pdb=" CA  PRO B  91 "
        pdb=" C   PRO B  91 "
      ideal   model   delta    sigma   weight residual
     110.55  101.15    9.40 1.63e+00 3.76e-01 3.33e+01
  angle pdb=" C   LEU B  96 "
        pdb=" N   PHE B  97 "
        pdb=" CA  PHE B  97 "
      ideal   model   delta    sigma   weight residual
     120.54  112.92    7.62 1.35e+00 5.49e-01 3.18e+01
  angle pdb=" C12 I2R A 201 "
        pdb=" C19 I2R A 201 "
        pdb=" C22 I2R A 201 "
      ideal   model   delta    sigma   weight residual
     122.00  137.90  -15.90 3.00e+00 1.11e-01 2.81e+01
  angle pdb=" N   TYR E  92 "
        pdb=" CA  TYR E  92 "
        pdb=" CB  TYR E  92 "
      ideal   model   delta    sigma   weight residual
     110.57  103.35    7.22 1.57e+00 4.06e-01 2.12e+01
  ... (remaining 7260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 2876
       17.88 -    35.75: 247
       35.75 -    53.63: 43
       53.63 -    71.50: 7
       71.50 -    89.38: 6
  Dihedral angle restraints: 3179
    sinusoidal: 1265
      harmonic: 1914
  Sorted by residual:
  dihedral pdb=" CA  SER A  47 "
           pdb=" C   SER A  47 "
           pdb=" N   PRO A  48 "
           pdb=" CA  PRO A  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.09  -25.91     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  PHE B  80 "
           pdb=" C   PHE B  80 "
           pdb=" N   ILE B  81 "
           pdb=" CA  ILE B  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.49   24.51     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CA  THR B  12 "
           pdb=" C   THR B  12 "
           pdb=" N   TYR B  13 "
           pdb=" CA  TYR B  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.10   22.90     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 3176 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 364
       0.054 -    0.108: 247
       0.108 -    0.162: 111
       0.162 -    0.216: 37
       0.216 -    0.269: 14
  Chirality restraints: 773
  Sorted by residual:
  chirality pdb=" CG  LEU C  18 "
            pdb=" CB  LEU C  18 "
            pdb=" CD1 LEU C  18 "
            pdb=" CD2 LEU C  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  VAL C  78 "
            pdb=" CA  VAL C  78 "
            pdb=" CG1 VAL C  78 "
            pdb=" CG2 VAL C  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CG  LEU B  52 "
            pdb=" CB  LEU B  52 "
            pdb=" CD1 LEU B  52 "
            pdb=" CD2 LEU B  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 770 not shown)

  Planarity restraints: 929
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  37 "    0.067 5.00e-02 4.00e+02   1.02e-01 1.66e+01
        pdb=" N   PRO B  38 "   -0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO B  38 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO B  38 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  29 "   -0.060 5.00e-02 4.00e+02   8.96e-02 1.28e+01
        pdb=" N   PRO B  30 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO B  30 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B  30 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  34 "    0.028 2.00e-02 2.50e+03   2.76e-02 1.14e+01
        pdb=" CG  HIS B  34 "   -0.059 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  34 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  34 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  34 "    0.004 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  34 "    0.009 2.00e-02 2.50e+03
  ... (remaining 926 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 822
        2.74 -     3.28: 4581
        3.28 -     3.82: 7666
        3.82 -     4.36: 9513
        4.36 -     4.90: 16024
  Nonbonded interactions: 38606
  Sorted by model distance:
  nonbonded pdb=" N   GLU B  26 "
            pdb=" OE1 GLU B  26 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" OG1 THR D  69 "
            pdb=" OG  SER F 444 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLU B 120 "
            pdb=" N   LYS B 124 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" NZ  LYS E  24 "
            pdb=" OD1 ASP E  76 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   LYS F 461 "
            pdb=" OG  SER F 465 "
     model   vdw
     2.227 3.040
  ... (remaining 38601 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.41 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.540
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
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      :  0.021   0.215   5370  Z= 0.937
  Angle     :  1.466  15.901   7271  Z= 0.856
  Chirality :  0.087   0.269    773
  Planarity :  0.011   0.102    929
  Dihedral  : 14.420  89.376   1948
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.56 %
    Favored  : 86.44 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  1.26 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.29 (0.28), residues: 650
  helix: -2.64 (0.28), residues: 219
  sheet: -1.89 (0.38), residues: 176
  loop : -3.59 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.005   TRP A  28 
 HIS   0.027   0.005   HIS B  34 
 PHE   0.041   0.005   PHE E 103 
 TYR   0.045   0.005   TYR A  71 
 ARG   0.012   0.001   ARG E  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29320 (  217)
  hydrogen bonds       : angle       9.49301 (  615)
  SS BOND              : bond        0.01975 (    3)
  SS BOND              : angle       1.80772 (    6)
  covalent geometry    : bond        0.02093 ( 5367)
  covalent geometry    : angle       1.46596 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.602 
Fit side-chains
REVERT: D   73 ASP cc_start: 0.7458 (t0) cc_final: 0.7198 (t0)
REVERT: E    3 MET cc_start: 0.6953 (mmm) cc_final: 0.6436 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 79
  average time/residue: 0.2125
  time to fit residues: 20.8674
Evaluate side-chains
  78 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  115 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
F 383 GLN
F 406 GLN
** F 432 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 = 0.3787 r_free = 0.3787 target = 0.140526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.115479 restraints weight = 7674.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.20
r_work: 0.3308 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5370  Z= 0.180
  Angle     :  0.740   8.494   7271  Z= 0.382
  Chirality :  0.044   0.138    773
  Planarity :  0.007   0.082    929
  Dihedral  :  6.270  48.290    743
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  7.58 %
    Favored  : 91.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.89 (0.31), residues: 650
  helix: -1.24 (0.33), residues: 219
  sheet: -1.31 (0.36), residues: 193
  loop : -2.95 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  34 
 HIS   0.010   0.002   HIS E  95 
 PHE   0.016   0.002   PHE D  29 
 TYR   0.018   0.002   TYR A  62 
 ARG   0.003   0.001   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07200 (  217)
  hydrogen bonds       : angle       5.87454 (  615)
  SS BOND              : bond        0.01039 (    3)
  SS BOND              : angle       1.70657 (    6)
  covalent geometry    : bond        0.00389 ( 5367)
  covalent geometry    : angle       0.73853 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.566 
Fit side-chains
REVERT: D   87 ARG cc_start: 0.7561 (mtt180) cc_final: 0.7330 (mtt180)
REVERT: E    3 MET cc_start: 0.8091 (mmm) cc_final: 0.7616 (mmm)
REVERT: C  120 GLU cc_start: 0.7883 (pt0) cc_final: 0.7678 (pt0)
  outliers start: 4
  outliers final: 3
  residues processed: 77
  average time/residue: 0.2094
  time to fit residues: 20.2504
Evaluate side-chains
  75 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 50 optimal weight:    0.4980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3773 r_free = 0.3773 target = 0.139390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.114212 restraints weight = 7774.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.20
r_work: 0.3310 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5370  Z= 0.180
  Angle     :  0.740   8.494   7271  Z= 0.382
  Chirality :  0.044   0.138    773
  Planarity :  0.007   0.082    929
  Dihedral  :  5.805  19.862    738
  Min Nonbonded Distance : 1.636

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  8.30 %
    Favored  : 91.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.89 (0.31), residues: 650
  helix: -1.24 (0.33), residues: 219
  sheet: -1.31 (0.36), residues: 193
  loop : -2.95 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  34 
 HIS   0.010   0.002   HIS E  95 
 PHE   0.016   0.002   PHE D  29 
 TYR   0.018   0.002   TYR A  62 
 ARG   0.003   0.001   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07200 (  217)
  hydrogen bonds       : angle       5.87454 (  615)
  SS BOND              : bond        0.01039 (    3)
  SS BOND              : angle       1.70680 (    6)
  covalent geometry    : bond        0.00389 ( 5367)
  covalent geometry    : angle       0.73842 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.592 
Fit side-chains
REVERT: D   87 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7352 (mtt180)
REVERT: E    3 MET cc_start: 0.8110 (mmm) cc_final: 0.7650 (mmm)
REVERT: C  120 GLU cc_start: 0.7899 (pt0) cc_final: 0.7693 (pt0)
  outliers start: 3
  outliers final: 3
  residues processed: 73
  average time/residue: 0.2146
  time to fit residues: 19.6823
Evaluate side-chains
  75 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0030
   chunk 40 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    0.3980
   chunk 16 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3788 r_free = 0.3788 target = 0.140207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.115278 restraints weight = 7924.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.22
r_work: 0.3320 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5370  Z= 0.158
  Angle     :  0.685   8.105   7271  Z= 0.352
  Chirality :  0.042   0.126    773
  Planarity :  0.006   0.068    929
  Dihedral  :  5.464  18.785    738
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  9.75 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.32), residues: 650
  helix: -0.71 (0.35), residues: 219
  sheet: -0.95 (0.37), residues: 190
  loop : -2.82 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  34 
 HIS   0.007   0.002   HIS E  95 
 PHE   0.013   0.001   PHE D  29 
 TYR   0.018   0.001   TYR A  62 
 ARG   0.015   0.001   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06663 (  217)
  hydrogen bonds       : angle       5.47650 (  615)
  SS BOND              : bond        0.00906 (    3)
  SS BOND              : angle       1.42787 (    6)
  covalent geometry    : bond        0.00336 ( 5367)
  covalent geometry    : angle       0.68385 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.578 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8102 (mmm) cc_final: 0.7639 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 72
  average time/residue: 0.2108
  time to fit residues: 19.0991
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0040
   chunk 58 optimal weight:    0.0970
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.9994

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.140584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.115713 restraints weight = 7779.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.18
r_work: 0.3325 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227   5370  Z= 0.272
  Angle     :  0.692   8.105   7271  Z= 0.355
  Chirality :  0.042   0.126    773
  Planarity :  0.006   0.068    929
  Dihedral  :  5.464  18.785    738
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 11.01 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.32), residues: 650
  helix: -0.71 (0.35), residues: 219
  sheet: -0.95 (0.37), residues: 190
  loop : -2.82 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  34 
 HIS   0.007   0.002   HIS E  95 
 PHE   0.013   0.001   PHE D  29 
 TYR   0.018   0.001   TYR A  62 
 ARG   0.015   0.001   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06663 (  217)
  hydrogen bonds       : angle       5.47650 (  615)
  SS BOND              : bond        0.00906 (    3)
  SS BOND              : angle       1.42791 (    6)
  covalent geometry    : bond        0.00458 ( 5367)
  covalent geometry    : angle       0.69106 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.525 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8103 (mmm) cc_final: 0.7643 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.2123
  time to fit residues: 19.0183
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3780 r_free = 0.3780 target = 0.139885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.114691 restraints weight = 7796.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.21
r_work: 0.3321 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227   5370  Z= 0.272
  Angle     :  0.692   8.105   7271  Z= 0.355
  Chirality :  0.042   0.126    773
  Planarity :  0.006   0.068    929
  Dihedral  :  5.464  18.785    738
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.83 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.32), residues: 650
  helix: -0.71 (0.35), residues: 219
  sheet: -0.95 (0.37), residues: 190
  loop : -2.82 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  34 
 HIS   0.007   0.002   HIS E  95 
 PHE   0.013   0.001   PHE D  29 
 TYR   0.018   0.001   TYR A  62 
 ARG   0.015   0.001   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06663 (  217)
  hydrogen bonds       : angle       5.47650 (  615)
  SS BOND              : bond        0.00906 (    3)
  SS BOND              : angle       1.42791 (    6)
  covalent geometry    : bond        0.00458 ( 5367)
  covalent geometry    : angle       0.69106 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.690 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8106 (mmm) cc_final: 0.7646 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.2306
  time to fit residues: 21.1488
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0970
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 17 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.140588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.115745 restraints weight = 7691.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.18
r_work: 0.3323 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227   5370  Z= 0.272
  Angle     :  0.692   8.105   7271  Z= 0.355
  Chirality :  0.042   0.126    773
  Planarity :  0.006   0.068    929
  Dihedral  :  5.464  18.785    738
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.83 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.32), residues: 650
  helix: -0.71 (0.35), residues: 219
  sheet: -0.95 (0.37), residues: 190
  loop : -2.82 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  34 
 HIS   0.007   0.002   HIS E  95 
 PHE   0.013   0.001   PHE D  29 
 TYR   0.018   0.001   TYR A  62 
 ARG   0.015   0.001   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06663 (  217)
  hydrogen bonds       : angle       5.47650 (  615)
  SS BOND              : bond        0.00906 (    3)
  SS BOND              : angle       1.42791 (    6)
  covalent geometry    : bond        0.00458 ( 5367)
  covalent geometry    : angle       0.69106 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.686 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8109 (mmm) cc_final: 0.7650 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.2086
  time to fit residues: 18.5453
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.140588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.115671 restraints weight = 7765.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.20
r_work: 0.3322 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227   5370  Z= 0.272
  Angle     :  0.692   8.105   7271  Z= 0.355
  Chirality :  0.042   0.126    773
  Planarity :  0.006   0.068    929
  Dihedral  :  5.464  18.785    738
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.83 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.32), residues: 650
  helix: -0.71 (0.35), residues: 219
  sheet: -0.95 (0.37), residues: 190
  loop : -2.82 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  34 
 HIS   0.007   0.002   HIS E  95 
 PHE   0.013   0.001   PHE D  29 
 TYR   0.018   0.001   TYR A  62 
 ARG   0.015   0.001   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06663 (  217)
  hydrogen bonds       : angle       5.47650 (  615)
  SS BOND              : bond        0.00906 (    3)
  SS BOND              : angle       1.42791 (    6)
  covalent geometry    : bond        0.00458 ( 5367)
  covalent geometry    : angle       0.69106 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.578 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8105 (mmm) cc_final: 0.7644 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.2141
  time to fit residues: 19.1253
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.0370
   chunk 58 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.140588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.115763 restraints weight = 7695.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.17
r_work: 0.3325 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227   5370  Z= 0.272
  Angle     :  0.692   8.105   7271  Z= 0.355
  Chirality :  0.042   0.126    773
  Planarity :  0.006   0.068    929
  Dihedral  :  5.464  18.785    738
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.83 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.32), residues: 650
  helix: -0.71 (0.35), residues: 219
  sheet: -0.95 (0.37), residues: 190
  loop : -2.82 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  34 
 HIS   0.007   0.002   HIS E  95 
 PHE   0.013   0.001   PHE D  29 
 TYR   0.018   0.001   TYR A  62 
 ARG   0.015   0.001   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06663 (  217)
  hydrogen bonds       : angle       5.47650 (  615)
  SS BOND              : bond        0.00906 (    3)
  SS BOND              : angle       1.42791 (    6)
  covalent geometry    : bond        0.00458 ( 5367)
  covalent geometry    : angle       0.69106 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.568 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8108 (mmm) cc_final: 0.7650 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.2246
  time to fit residues: 20.0193
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0030
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.140588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.115685 restraints weight = 7745.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.19
r_work: 0.3322 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227   5370  Z= 0.272
  Angle     :  0.692   8.105   7271  Z= 0.355
  Chirality :  0.042   0.126    773
  Planarity :  0.006   0.068    929
  Dihedral  :  5.464  18.785    738
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.83 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.32), residues: 650
  helix: -0.71 (0.35), residues: 219
  sheet: -0.95 (0.37), residues: 190
  loop : -2.82 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  34 
 HIS   0.007   0.002   HIS E  95 
 PHE   0.013   0.001   PHE D  29 
 TYR   0.018   0.001   TYR A  62 
 ARG   0.015   0.001   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06663 (  217)
  hydrogen bonds       : angle       5.47650 (  615)
  SS BOND              : bond        0.00906 (    3)
  SS BOND              : angle       1.42791 (    6)
  covalent geometry    : bond        0.00458 ( 5367)
  covalent geometry    : angle       0.69106 ( 7265)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.682 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8106 (mmm) cc_final: 0.7644 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 71
  average time/residue: 0.2137
  time to fit residues: 19.0387
Evaluate side-chains
  72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain C residue    2 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0570
   chunk 11 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0040
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    7.9990
   chunk 46 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0030
   overall best weight:    0.2720

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

Flipped N/Q/H residues before XYZ refinement:
** F 432 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.140588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.115691 restraints weight = 7737.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.19
r_work: 0.3322 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227   5370  Z= 0.272
  Angle     :  0.692   8.105   7271  Z= 0.355
  Chirality :  0.042   0.126    773
  Planarity :  0.006   0.068    929
  Dihedral  :  5.464  18.785    738
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.83 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.37 (0.32), residues: 650
  helix: -0.71 (0.35), residues: 219
  sheet: -0.95 (0.37), residues: 190
  loop : -2.82 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  34 
 HIS   0.007   0.002   HIS E  95 
 PHE   0.013   0.001   PHE D  29 
 TYR   0.018   0.001   TYR A  62 
 ARG   0.015   0.001   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06663 (  217)
  hydrogen bonds       : angle       5.47650 (  615)
  SS BOND              : bond        0.00906 (    3)
  SS BOND              : angle       1.42791 (    6)
  covalent geometry    : bond        0.00458 ( 5367)
  covalent geometry    : angle       0.69106 ( 7265)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3759.11 seconds
wall clock time: 65 minutes 40.80 seconds (3940.80 seconds total)