Starting phenix.real_space_refine
on Wed Sep 17 05:44:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mnx_48442/09_2025/9mnx_48442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mnx_48442/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mnx_48442/09_2025/9mnx_48442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mnx_48442/09_2025/9mnx_48442.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mnx_48442/09_2025/9mnx_48442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mnx_48442/09_2025/9mnx_48442.map"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.44, per 1000 atoms: 0.27
  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: 0.65
  Conformation dependent library (CDL) restraints added in 224.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.21
  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: 0.75

  Time building geometry restraints manager: 0.79 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.890
-------------------------------------------------------------------------------
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 : 11.97
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.012   0.001   ARG E  18 
 TYR   0.045   0.005   TYR A  71 
 PHE   0.041   0.005   PHE E 103 
 TRP   0.031   0.005   TRP A  28 
 HIS   0.027   0.005   HIS B  34 

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

*********************** 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  : 0.210 
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: 0.1017
  time to fit residues: 9.9928
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  : 0.199 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    0.3980
   overall best weight:    0.7382

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.139371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.114304 restraints weight = 7746.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.20
r_work: 0.3304 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5370  Z= 0.212
  Angle     :  0.767   8.284   7271  Z= 0.398
  Chirality :  0.046   0.147    773
  Planarity :  0.008   0.084    929
  Dihedral  :  6.374  48.956    743
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  7.94 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.97 (0.31), residues: 650
  helix: -1.34 (0.33), residues: 219
  sheet: -1.32 (0.36), residues: 193
  loop : -2.99 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  62 
 TYR   0.019   0.002   TYR A  62 
 PHE   0.017   0.002   PHE D  29 
 TRP   0.014   0.002   TRP A  34 
 HIS   0.012   0.002   HIS E  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 5367)
  covalent geometry    : angle       0.76565 ( 7265)
  SS BOND              : bond        0.01173 (    3)
  SS BOND              : angle       1.90790 (    6)
  hydrogen bonds       : bond        0.07671 (  217)
  hydrogen bonds       : angle       5.97317 (  615)

*********************** 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
  78 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.200 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8111 (mmm) cc_final: 0.7643 (mmm)
REVERT: C  120 GLU cc_start: 0.7905 (pt0) cc_final: 0.7700 (pt0)
  outliers start: 4
  outliers final: 3
  residues processed: 76
  average time/residue: 0.1020
  time to fit residues: 9.6260
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  : 0.213 
-------------------------------------------------------------------------------
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 28 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0270
   chunk 16 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   overall best weight:    0.4438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.138191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.112935 restraints weight = 7859.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.22
r_work: 0.3296 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5370  Z= 0.212
  Angle     :  0.767   8.284   7271  Z= 0.398
  Chirality :  0.046   0.147    773
  Planarity :  0.008   0.084    929
  Dihedral  :  5.893  20.211    738
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  8.84 %
    Favored  : 90.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.97 (0.31), residues: 650
  helix: -1.34 (0.33), residues: 219
  sheet: -1.32 (0.36), residues: 193
  loop : -2.99 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  62 
 TYR   0.019   0.002   TYR A  62 
 PHE   0.017   0.002   PHE D  29 
 TRP   0.014   0.002   TRP A  34 
 HIS   0.012   0.002   HIS E  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 5367)
  covalent geometry    : angle       0.76565 ( 7265)
  SS BOND              : bond        0.01173 (    3)
  SS BOND              : angle       1.90790 (    6)
  hydrogen bonds       : bond        0.07671 (  217)
  hydrogen bonds       : angle       5.97317 (  615)

*********************** 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
  73 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.235 
Fit side-chains
REVERT: E    3 MET cc_start: 0.8128 (mmm) cc_final: 0.7671 (mmm)
REVERT: C  120 GLU cc_start: 0.7919 (pt0) cc_final: 0.7716 (pt0)
  outliers start: 3
  outliers final: 3
  residues processed: 71
  average time/residue: 0.1070
  time to fit residues: 9.5025
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  : 0.202 
-------------------------------------------------------------------------------
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 15 optimal weight:    0.9980
   chunk 50 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0370
   chunk 54 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0870
   chunk 34 optimal weight:    0.0980
   chunk 53 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0170
   overall best weight:    0.1474

-------------------------------------------------------------------------------
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 = 0.3822 r_free = 0.3822 target = 0.142982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.118290 restraints weight = 7771.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.17
r_work: 0.3355 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5370  Z= 0.124
  Angle     :  0.616   6.629   7271  Z= 0.314
  Chirality :  0.040   0.127    773
  Planarity :  0.006   0.071    929
  Dihedral  :  5.048  18.106    738
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.57 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.32), residues: 650
  helix: -0.36 (0.36), residues: 221
  sheet: -0.84 (0.36), residues: 190
  loop : -2.82 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 438 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.011   0.001   PHE D  29 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.003   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5367)
  covalent geometry    : angle       0.61571 ( 7265)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.06185 (    6)
  hydrogen bonds       : bond        0.05493 (  217)
  hydrogen bonds       : angle       5.04179 (  615)

*********************** 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
  71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7675 (mtpt)
REVERT: D   87 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7274 (mtt180)
REVERT: E    3 MET cc_start: 0.8106 (mmm) cc_final: 0.7650 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 68
  average time/residue: 0.1007
  time to fit residues: 8.5248
Evaluate side-chains
  69 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0570
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3821 r_free = 0.3821 target = 0.142925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.117706 restraints weight = 7919.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.24
r_work: 0.3348 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5370  Z= 0.124
  Angle     :  0.616   6.629   7271  Z= 0.314
  Chirality :  0.040   0.127    773
  Planarity :  0.006   0.071    929
  Dihedral  :  5.050  18.106    738
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.37 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.32), residues: 650
  helix: -0.36 (0.36), residues: 221
  sheet: -0.84 (0.36), residues: 190
  loop : -2.82 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 438 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.011   0.001   PHE D  29 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.003   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5367)
  covalent geometry    : angle       0.61571 ( 7265)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.06187 (    6)
  hydrogen bonds       : bond        0.05493 (  217)
  hydrogen bonds       : angle       5.04179 (  615)

*********************** 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
  69 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.176 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7676 (mtpt)
REVERT: D   87 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7278 (mtt180)
REVERT: E    3 MET cc_start: 0.8115 (mmm) cc_final: 0.7660 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 67
  average time/residue: 0.1019
  time to fit residues: 8.5330
Evaluate side-chains
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 37 optimal weight:    0.2980
   chunk 33 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0270
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3821 r_free = 0.3821 target = 0.142918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.117790 restraints weight = 7848.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.22
r_work: 0.3349 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5370  Z= 0.124
  Angle     :  0.616   6.629   7271  Z= 0.314
  Chirality :  0.040   0.127    773
  Planarity :  0.006   0.071    929
  Dihedral  :  5.048  18.106    738
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.55 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.32), residues: 650
  helix: -0.36 (0.36), residues: 221
  sheet: -0.84 (0.36), residues: 190
  loop : -2.82 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 438 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.011   0.001   PHE D  29 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.003   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5367)
  covalent geometry    : angle       0.61571 ( 7265)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.06187 (    6)
  hydrogen bonds       : bond        0.05493 (  217)
  hydrogen bonds       : angle       5.04179 (  615)

*********************** 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
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.190 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7681 (mtpt)
REVERT: D   87 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7273 (mtt180)
REVERT: E    3 MET cc_start: 0.8118 (mmm) cc_final: 0.7665 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 66
  average time/residue: 0.1022
  time to fit residues: 8.4461
Evaluate side-chains
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 7 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    0.1980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3821 r_free = 0.3821 target = 0.142909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.117788 restraints weight = 7842.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.22
r_work: 0.3351 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5370  Z= 0.124
  Angle     :  0.616   6.629   7271  Z= 0.314
  Chirality :  0.040   0.127    773
  Planarity :  0.006   0.071    929
  Dihedral  :  5.048  18.106    738
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.55 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.32), residues: 650
  helix: -0.36 (0.36), residues: 221
  sheet: -0.84 (0.36), residues: 190
  loop : -2.82 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 438 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.011   0.001   PHE D  29 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.003   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5367)
  covalent geometry    : angle       0.61571 ( 7265)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.06187 (    6)
  hydrogen bonds       : bond        0.05493 (  217)
  hydrogen bonds       : angle       5.04179 (  615)

*********************** 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
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.174 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7673 (mtpt)
REVERT: D   87 ARG cc_start: 0.7499 (mtt180) cc_final: 0.7282 (mtt180)
REVERT: E    3 MET cc_start: 0.8114 (mmm) cc_final: 0.7660 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 66
  average time/residue: 0.0895
  time to fit residues: 7.4608
Evaluate side-chains
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 24 optimal weight:    0.1980
   chunk 14 optimal weight:    0.0980
   chunk 62 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0010
   chunk 56 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.2986

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3821 r_free = 0.3821 target = 0.142908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.117829 restraints weight = 7828.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.21
r_work: 0.3352 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5370  Z= 0.124
  Angle     :  0.616   6.629   7271  Z= 0.314
  Chirality :  0.040   0.127    773
  Planarity :  0.006   0.071    929
  Dihedral  :  5.048  18.106    738
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.55 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.32), residues: 650
  helix: -0.36 (0.36), residues: 221
  sheet: -0.84 (0.36), residues: 190
  loop : -2.82 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 438 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.011   0.001   PHE D  29 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.003   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5367)
  covalent geometry    : angle       0.61571 ( 7265)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.06187 (    6)
  hydrogen bonds       : bond        0.05493 (  217)
  hydrogen bonds       : angle       5.04179 (  615)

*********************** 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
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.168 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7672 (mtpt)
REVERT: D   87 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7281 (mtt180)
REVERT: E    3 MET cc_start: 0.8115 (mmm) cc_final: 0.7661 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 66
  average time/residue: 0.1036
  time to fit residues: 8.5078
Evaluate side-chains
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0980
   chunk 58 optimal weight:    0.0000
   chunk 48 optimal weight:    0.7980
   chunk 1 optimal weight:    0.1980
   chunk 15 optimal weight:    0.1980
   overall best weight:    0.2184

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3821 r_free = 0.3821 target = 0.142908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.117820 restraints weight = 7849.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.21
r_work: 0.3352 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5370  Z= 0.124
  Angle     :  0.616   6.629   7271  Z= 0.314
  Chirality :  0.040   0.127    773
  Planarity :  0.006   0.071    929
  Dihedral  :  5.048  18.106    738
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.55 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.32), residues: 650
  helix: -0.36 (0.36), residues: 221
  sheet: -0.84 (0.36), residues: 190
  loop : -2.82 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 438 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.011   0.001   PHE D  29 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.003   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5367)
  covalent geometry    : angle       0.61571 ( 7265)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.06187 (    6)
  hydrogen bonds       : bond        0.05493 (  217)
  hydrogen bonds       : angle       5.04179 (  615)

*********************** 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
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.201 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7671 (mtpt)
REVERT: D   87 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7276 (mtt180)
REVERT: E    3 MET cc_start: 0.8123 (mmm) cc_final: 0.7669 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 66
  average time/residue: 0.1059
  time to fit residues: 8.6849
Evaluate side-chains
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 50 optimal weight:    0.2980
   chunk 32 optimal weight:    0.0980
   chunk 61 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 20 optimal weight:    0.2980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3821 r_free = 0.3821 target = 0.142908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.117831 restraints weight = 7831.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.20
r_work: 0.3352 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5370  Z= 0.124
  Angle     :  0.616   6.629   7271  Z= 0.314
  Chirality :  0.040   0.127    773
  Planarity :  0.006   0.071    929
  Dihedral  :  5.048  18.106    738
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.55 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.32), residues: 650
  helix: -0.36 (0.36), residues: 221
  sheet: -0.84 (0.36), residues: 190
  loop : -2.82 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 438 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.011   0.001   PHE D  29 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.003   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5367)
  covalent geometry    : angle       0.61571 ( 7265)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.06187 (    6)
  hydrogen bonds       : bond        0.05493 (  217)
  hydrogen bonds       : angle       5.04179 (  615)

********************** 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
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.211 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7674 (mtpt)
REVERT: D   87 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7279 (mtt180)
REVERT: E    3 MET cc_start: 0.8114 (mmm) cc_final: 0.7658 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 66
  average time/residue: 0.1108
  time to fit residues: 9.0739
Evaluate side-chains
  68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3821 r_free = 0.3821 target = 0.142907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.117788 restraints weight = 7851.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.22
r_work: 0.3351 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5370  Z= 0.124
  Angle     :  0.616   6.629   7271  Z= 0.314
  Chirality :  0.040   0.127    773
  Planarity :  0.006   0.071    929
  Dihedral  :  5.048  18.106    738
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.55 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.32), residues: 650
  helix: -0.36 (0.36), residues: 221
  sheet: -0.84 (0.36), residues: 190
  loop : -2.82 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 438 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.011   0.001   PHE D  29 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.003   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5367)
  covalent geometry    : angle       0.61571 ( 7265)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.06187 (    6)
  hydrogen bonds       : bond        0.05493 (  217)
  hydrogen bonds       : angle       5.04179 (  615)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2008.20 seconds
wall clock time: 35 minutes 4.72 seconds (2104.72 seconds total)