Starting phenix.real_space_refine
on Sat Aug 23 08:56:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hq7_34946/08_2025/8hq7_34946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hq7_34946/08_2025/8hq7_34946.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hq7_34946/08_2025/8hq7_34946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hq7_34946/08_2025/8hq7_34946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hq7_34946/08_2025/8hq7_34946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hq7_34946/08_2025/8hq7_34946.cif"
  }
  resolution = 2.7
  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=   0.000 sd=   0.039
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 3142 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      34      5.16       5
     C    5221      2.51       5
     N    1387      2.21       5
     O    1650      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8292
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "M"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1665
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
    Chain: "N"
      Number of atoms: 1642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1642
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204}
    Chain: "H"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1756
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214}
    Chain: "L"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1658
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.27, per 1000 atoms: 0.27
  Number of scatterers: 8292
  At special positions: 0
  Unit cell: (136.96, 93.304, 124.12, 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      34     16.00
     O    1650      8.00
     N    1387      7.00
     C    5221      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 149 " - pdb=" SG  CYS M 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 225 " - pdb=" SG  CYS N 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 136 " - pdb=" SG  CYS N 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 155 " - pdb=" SG  CYS H 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 231 " - pdb=" SG  CYS L 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.04

  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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 442.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1996

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 24 sheets defined
      9.7% alpha, 44.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.709A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.957A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.428A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'M' and resid 28 through 32
    Processing helix  chain 'M' and resid 86 through 90
    Processing helix  chain 'M' and resid 165 through 167
      No H-bonds generated for 'chain 'M' and resid 165 through 167'
    Processing helix  chain 'M' and resid 194 through 199
      removed outlier: 4.071A  pdb=" N   GLY M 199 " --> pdb=" O   SER M 196 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 79 through 83
      removed outlier: 4.233A  pdb=" N   PHE N  83 " --> pdb=" O   PRO N  80 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 123 through 129
      removed outlier: 4.058A  pdb=" N   SER N 129 " --> pdb=" O   GLU N 125 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 185 through 190
      removed outlier: 3.988A  pdb=" N   LYS N 190 " --> pdb=" O   ALA N 186 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 67
      removed outlier: 3.560A  pdb=" N   ASN H  66 " --> pdb=" O   PRO H  63 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   ASN H  67 " --> pdb=" O   SER H  64 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 63 through 67'
    Processing helix  chain 'H' and resid 171 through 173
      No H-bonds generated for 'chain 'H' and resid 171 through 173'
    Processing helix  chain 'H' and resid 200 through 204
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.160A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'M' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'M' and resid 10 through 12
      removed outlier: 6.089A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 119 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   TYR M  33 " --> pdb=" O   GLU M  98 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   ARG M  38 " --> pdb=" O   TRP M  47 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   TRP M  47 " --> pdb=" O   ARG M  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'M' and resid 10 through 12
      removed outlier: 6.089A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 119 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ILE M 111 " --> pdb=" O   ARG M  97 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   SER M  99 " --> pdb=" O   PHE M 109 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   PHE M 109 " --> pdb=" O   SER M  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'M' and resid 129 through 133
      removed outlier: 6.023A  pdb=" N   TYR M 185 " --> pdb=" O   ASP M 153 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'M' and resid 129 through 133
      removed outlier: 6.023A  pdb=" N   TYR M 185 " --> pdb=" O   ASP M 153 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'M' and resid 160 through 163
    Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.574A  pdb=" N   ASP N  70 " --> pdb=" O   SER N  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.942A  pdb=" N   LEU N  33 " --> pdb=" O   SER N  49 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   SER N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 13
      removed outlier: 4.014A  pdb=" N   SER N  99 " --> pdb=" O   GLN N  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 116 through 120
      removed outlier: 6.137A  pdb=" N   TYR N 175 " --> pdb=" O   ASN N 140 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 155 through 156
    Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.171A  pdb=" N   ARG H  40 " --> pdb=" O   TRP H  49 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   TRP H  49 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 7.529A  pdb=" N   PHE H 101 " --> pdb=" O   PHE H 115 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   PHE H 115 " --> pdb=" O   PHE H 101 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 135 through 139
      removed outlier: 6.413A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 135 through 139
      removed outlier: 6.413A  pdb=" N   TYR H 191 " --> pdb=" O   ASP H 159 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER H 192 " --> pdb=" O   VAL H 184 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 166 through 169
      removed outlier: 3.849A  pdb=" N   TYR H 209 " --> pdb=" O   VAL H 226 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.989A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 115 through 119
      removed outlier: 5.915A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 146 through 151

    361 hydrogen bonds defined for protein.
    891 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: 1.53

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2658
        1.35 -     1.47: 2174
        1.47 -     1.59: 3621
        1.59 -     1.71: 0
        1.71 -     1.83: 40
  Bond restraints: 8493
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" CA  CYS A 379 "
       pdb=" CB  CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.534  1.512  0.022 1.78e-02 3.16e+03 1.50e+00
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.29e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.12e+00
  bond pdb=" C3  NAG B   2 "
       pdb=" O3  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.01e+00
  ... (remaining 8488 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.96: 11523
        3.96 -     7.91: 33
        7.91 -    11.87: 2
       11.87 -    15.82: 0
       15.82 -    19.78: 2
  Bond angle restraints: 11560
  Sorted by residual:
  angle pdb=" CA  CYS A 432 "
        pdb=" CB  CYS A 432 "
        pdb=" SG  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     114.40  134.18  -19.78 2.30e+00 1.89e-01 7.40e+01
  angle pdb=" CA  CYS A 379 "
        pdb=" CB  CYS A 379 "
        pdb=" SG  CYS A 379 "
      ideal   model   delta    sigma   weight residual
     114.40  133.94  -19.54 2.30e+00 1.89e-01 7.22e+01
  angle pdb=" N   CYS A 379 "
        pdb=" CA  CYS A 379 "
        pdb=" C   CYS A 379 "
      ideal   model   delta    sigma   weight residual
     108.99  117.53   -8.54 1.57e+00 4.06e-01 2.96e+01
  angle pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
        pdb=" C   CYS A 432 "
      ideal   model   delta    sigma   weight residual
     108.60  115.16   -6.56 1.46e+00 4.69e-01 2.02e+01
  angle pdb=" C   PRO H  14 "
        pdb=" N   THR H  15 "
        pdb=" CA  THR H  15 "
      ideal   model   delta    sigma   weight residual
     122.08  127.66   -5.58 1.47e+00 4.63e-01 1.44e+01
  ... (remaining 11555 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 4661
       16.21 -    32.42: 331
       32.42 -    48.62: 80
       48.62 -    64.83: 20
       64.83 -    81.04: 12
  Dihedral angle restraints: 5104
    sinusoidal: 1980
      harmonic: 3124
  Sorted by residual:
  dihedral pdb=" CA  ASP H 116 "
           pdb=" C   ASP H 116 "
           pdb=" N   PRO H 117 "
           pdb=" CA  PRO H 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -130.92  -49.08     0      5.00e+00 4.00e-02 9.64e+01
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -4.96  -81.04     1      1.00e+01 1.00e-02 8.10e+01
  dihedral pdb=" CB  CYS M 149 "
           pdb=" SG  CYS M 149 "
           pdb=" SG  CYS M 205 "
           pdb=" CB  CYS M 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.58  -80.58     1      1.00e+01 1.00e-02 8.03e+01
  ... (remaining 5101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1181
       0.083 -    0.167: 114
       0.167 -    0.250: 1
       0.250 -    0.333: 1
       0.333 -    0.417: 1
  Chirality restraints: 1298
  Sorted by residual:
  chirality pdb=" CA  CYS A 379 "
            pdb=" N   CYS A 379 "
            pdb=" C   CYS A 379 "
            pdb=" CB  CYS A 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.34e+00
  chirality pdb=" CA  CYS A 432 "
            pdb=" N   CYS A 432 "
            pdb=" C   CYS A 432 "
            pdb=" CB  CYS A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  THR H  15 "
            pdb=" N   THR H  15 "
            pdb=" C   THR H  15 "
            pdb=" CB  THR H  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.64e-01
  ... (remaining 1295 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H 116 "    0.057 5.00e-02 4.00e+02   8.59e-02 1.18e+01
        pdb=" N   PRO H 117 "   -0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO H 117 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO H 117 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU M 157 "    0.051 5.00e-02 4.00e+02   7.81e-02 9.76e+00
        pdb=" N   PRO M 158 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO M 158 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO M 158 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU L  80 "    0.032 5.00e-02 4.00e+02   4.90e-02 3.84e+00
        pdb=" N   PRO L  81 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO L  81 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO L  81 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 141
        2.68 -     3.24: 7354
        3.24 -     3.79: 12087
        3.79 -     4.35: 16965
        4.35 -     4.90: 28668
  Nonbonded interactions: 65215
  Sorted by model distance:
  nonbonded pdb=" OG  SER L 163 "
            pdb=" OG  SER L 177 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OD2 ASP N 172 "
            pdb=" OG1 THR N 174 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" CB  CYS A 379 "
            pdb=" CB  CYS A 432 "
     model   vdw
     2.212 3.072
  nonbonded pdb=" OD1 ASP M  61 "
            pdb=" NH2 ARG N  96 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" OG1 THR M 200 "
            pdb=" OE1 GLN M 201 "
     model   vdw
     2.301 3.040
  ... (remaining 65210 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=1.00 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:                  0.010
  Normalize map: mean=0, sd=1:             12.040
  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:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.640
  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:7.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
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      :  0.003   0.033   8509  Z= 0.152
  Angle     :  0.738  19.780  11594  Z= 0.379
  Chirality :  0.047   0.417   1298
  Planarity :  0.006   0.086   1487
  Dihedral  : 12.536  77.415   3066
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.26), residues: 1072
  helix: -2.67 (0.55), residues: 57
  sheet:  1.41 (0.25), residues: 452
  loop : -0.61 (0.27), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  60 
 TYR   0.015   0.002   TYR H 160 
 PHE   0.011   0.001   PHE N 211 
 TRP   0.011   0.001   TRP H 118 
 HIS   0.004   0.001   HIS N 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8493)
  covalent geometry    : angle       0.71975 (11560)
  SS BOND              : bond        0.00837 (   14)
  SS BOND              : angle       3.38717 (   28)
  hydrogen bonds       : bond        0.10947 (  317)
  hydrogen bonds       : angle       6.52206 (  891)
  link_BETA1-4         : bond        0.00232 (    1)
  link_BETA1-4         : angle       0.99809 (    3)
  link_NAG-ASN         : bond        0.00005 (    1)
  link_NAG-ASN         : angle       1.09992 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: M  208 ASN cc_start: 0.7153 (m110) cc_final: 0.6844 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.8565
  time to fit residues: 105.5347
Evaluate side-chains
  94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
M  13 GLN
M 208 ASN
N 162 GLN
H  66 ASN
L 125 GLN
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.144635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.104888 restraints weight = 13292.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.41
r_work: 0.3247 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.0859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8509  Z= 0.148
  Angle     :  0.665  14.620  11594  Z= 0.345
  Chirality :  0.046   0.222   1298
  Planarity :  0.006   0.083   1487
  Dihedral  :  5.505  55.323   1209
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  6.63 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1072
  helix: -2.72 (0.52), residues: 58
  sheet:  1.48 (0.25), residues: 449
  loop : -0.62 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 408 
 TYR   0.014   0.002   TYR N 194 
 PHE   0.010   0.001   PHE N 211 
 TRP   0.009   0.001   TRP N 150 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8493)
  covalent geometry    : angle       0.65302 (11560)
  SS BOND              : bond        0.00676 (   14)
  SS BOND              : angle       2.63989 (   28)
  hydrogen bonds       : bond        0.03935 (  317)
  hydrogen bonds       : angle       5.65152 (  891)
  link_BETA1-4         : bond        0.00362 (    1)
  link_BETA1-4         : angle       1.05635 (    3)
  link_NAG-ASN         : bond        0.00030 (    1)
  link_NAG-ASN         : angle       1.18437 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: M   75 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8679 (mttp)
REVERT: M  208 ASN cc_start: 0.7257 (m-40) cc_final: 0.6970 (m110)
REVERT: H  105 ASP cc_start: 0.8232 (p0) cc_final: 0.7959 (p0)
REVERT: L   18 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7829 (ttm-80)
REVERT: L  166 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5553 (pp20)
  outliers start: 12
  outliers final: 2
  residues processed: 97
  average time/residue: 0.8249
  time to fit residues: 83.7461
Evaluate side-chains
  90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain H residue   67 ASN
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain L residue  166 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0020
   chunk 104 optimal weight:    6.9990
   chunk 72 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
N 162 GLN
N 191 HIS
H 212 ASN
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.144873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.105563 restraints weight = 13231.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.35
r_work: 0.3259 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8509  Z= 0.132
  Angle     :  0.637  15.089  11594  Z= 0.330
  Chirality :  0.045   0.229   1298
  Planarity :  0.005   0.079   1487
  Dihedral  :  5.242  50.983   1209
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.95 %
    Favored  : 88.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.26), residues: 1072
  helix: -2.82 (0.53), residues: 57
  sheet:  1.50 (0.25), residues: 449
  loop : -0.61 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.013   0.001   TYR H 160 
 PHE   0.009   0.001   PHE N 211 
 TRP   0.008   0.001   TRP H 118 
 HIS   0.007   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8493)
  covalent geometry    : angle       0.62565 (11560)
  SS BOND              : bond        0.00585 (   14)
  SS BOND              : angle       2.47038 (   28)
  hydrogen bonds       : bond        0.03703 (  317)
  hydrogen bonds       : angle       5.48514 (  891)
  link_BETA1-4         : bond        0.00186 (    1)
  link_BETA1-4         : angle       1.15840 (    3)
  link_NAG-ASN         : bond        0.00023 (    1)
  link_NAG-ASN         : angle       1.16995 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: M   75 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8667 (mttp)
REVERT: M  208 ASN cc_start: 0.7215 (m-40) cc_final: 0.7000 (m110)
REVERT: M  215 LYS cc_start: 0.5463 (mmtm) cc_final: 0.4717 (tptt)
REVERT: N  191 HIS cc_start: 0.4099 (m-70) cc_final: 0.3861 (m-70)
REVERT: H   91 ASP cc_start: 0.7938 (m-30) cc_final: 0.7716 (m-30)
REVERT: H  105 ASP cc_start: 0.8087 (p0) cc_final: 0.7690 (p0)
REVERT: L   18 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7649 (ttm-80)
  outliers start: 16
  outliers final: 7
  residues processed: 99
  average time/residue: 0.7914
  time to fit residues: 82.0126
Evaluate side-chains
  90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue  108 ILE
Chi-restraints excluded: chain N residue  109 LYS
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain H residue   67 ASN
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.143769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.104204 restraints weight = 13416.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.31
r_work: 0.3248 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8509  Z= 0.154
  Angle     :  0.657  11.958  11594  Z= 0.341
  Chirality :  0.046   0.208   1298
  Planarity :  0.005   0.080   1487
  Dihedral  :  5.238  49.065   1209
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 10.37 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.26), residues: 1072
  helix: -2.57 (0.58), residues: 51
  sheet:  1.47 (0.25), residues: 457
  loop : -0.71 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  55 
 TYR   0.015   0.002   TYR H  96 
 PHE   0.010   0.001   PHE L 119 
 TRP   0.008   0.001   TRP N 150 
 HIS   0.008   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8493)
  covalent geometry    : angle       0.64667 (11560)
  SS BOND              : bond        0.00663 (   14)
  SS BOND              : angle       2.45354 (   28)
  hydrogen bonds       : bond        0.03919 (  317)
  hydrogen bonds       : angle       5.49525 (  891)
  link_BETA1-4         : bond        0.00203 (    1)
  link_BETA1-4         : angle       1.23069 (    3)
  link_NAG-ASN         : bond        0.00014 (    1)
  link_NAG-ASN         : angle       1.17134 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   75 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8690 (mttp)
REVERT: M  215 LYS cc_start: 0.5427 (mmtm) cc_final: 0.4707 (tptt)
REVERT: N  191 HIS cc_start: 0.4193 (m-70) cc_final: 0.3968 (m-70)
REVERT: H  105 ASP cc_start: 0.8161 (p0) cc_final: 0.7812 (p0)
REVERT: L  166 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5364 (pp20)
REVERT: L  195 CYS cc_start: 0.4767 (OUTLIER) cc_final: 0.4384 (t)
  outliers start: 27
  outliers final: 7
  residues processed: 99
  average time/residue: 0.7530
  time to fit residues: 78.3004
Evaluate side-chains
  88 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0070
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.144440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.105060 restraints weight = 13397.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.29
r_work: 0.3259 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8509  Z= 0.132
  Angle     :  0.634  14.870  11594  Z= 0.328
  Chirality :  0.045   0.247   1298
  Planarity :  0.005   0.078   1487
  Dihedral  :  4.999  47.867   1209
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.16 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1072
  helix: -2.79 (0.54), residues: 57
  sheet:  1.51 (0.25), residues: 449
  loop : -0.65 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  55 
 TYR   0.013   0.001   TYR H 160 
 PHE   0.010   0.001   PHE N 211 
 TRP   0.008   0.001   TRP H 118 
 HIS   0.009   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8493)
  covalent geometry    : angle       0.62302 (11560)
  SS BOND              : bond        0.00638 (   14)
  SS BOND              : angle       2.47549 (   28)
  hydrogen bonds       : bond        0.03641 (  317)
  hydrogen bonds       : angle       5.39931 (  891)
  link_BETA1-4         : bond        0.00257 (    1)
  link_BETA1-4         : angle       1.33626 (    3)
  link_NAG-ASN         : bond        0.00062 (    1)
  link_NAG-ASN         : angle       1.09029 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   75 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8656 (mttp)
REVERT: M  215 LYS cc_start: 0.5274 (mmtm) cc_final: 0.4703 (tptt)
REVERT: N   79 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7277 (mp10)
REVERT: N  191 HIS cc_start: 0.4331 (m-70) cc_final: 0.4066 (m-70)
REVERT: H  105 ASP cc_start: 0.8061 (p0) cc_final: 0.7683 (p0)
REVERT: L  166 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5274 (pp20)
REVERT: L  195 CYS cc_start: 0.4752 (OUTLIER) cc_final: 0.4388 (t)
  outliers start: 15
  outliers final: 4
  residues processed: 93
  average time/residue: 0.7084
  time to fit residues: 69.1550
Evaluate side-chains
  88 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue   79 GLN
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 104 optimal weight:    6.9990
   chunk 94 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 96 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
H  66 ASN
** L 211 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 = 0.3962 r_free = 0.3962 target = 0.144066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.104826 restraints weight = 13201.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.23
r_work: 0.3255 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8509  Z= 0.139
  Angle     :  0.643  13.028  11594  Z= 0.333
  Chirality :  0.046   0.231   1298
  Planarity :  0.005   0.078   1487
  Dihedral  :  4.892  48.123   1209
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.83 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1072
  helix: -2.51 (0.60), residues: 51
  sheet:  1.50 (0.25), residues: 450
  loop : -0.70 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  78 
 TYR   0.013   0.002   TYR H 109 
 PHE   0.010   0.001   PHE N 211 
 TRP   0.007   0.001   TRP H 169 
 HIS   0.009   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8493)
  covalent geometry    : angle       0.63224 (11560)
  SS BOND              : bond        0.00663 (   14)
  SS BOND              : angle       2.43488 (   28)
  hydrogen bonds       : bond        0.03718 (  317)
  hydrogen bonds       : angle       5.39018 (  891)
  link_BETA1-4         : bond        0.00258 (    1)
  link_BETA1-4         : angle       1.41735 (    3)
  link_NAG-ASN         : bond        0.00063 (    1)
  link_NAG-ASN         : angle       1.09982 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8333 (m) cc_final: 0.8098 (p)
REVERT: M    3 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7949 (tt0)
REVERT: M   75 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8671 (mttp)
REVERT: M  215 LYS cc_start: 0.5323 (mmtm) cc_final: 0.4734 (tptt)
REVERT: N  191 HIS cc_start: 0.4314 (m-70) cc_final: 0.4061 (m-70)
REVERT: H  105 ASP cc_start: 0.8090 (p0) cc_final: 0.7741 (p0)
REVERT: L   78 ARG cc_start: 0.7054 (mmm160) cc_final: 0.5991 (tpt-90)
REVERT: L  166 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5301 (pp20)
REVERT: L  195 CYS cc_start: 0.4790 (OUTLIER) cc_final: 0.4451 (t)
  outliers start: 24
  outliers final: 9
  residues processed: 96
  average time/residue: 0.6904
  time to fit residues: 69.6304
Evaluate side-chains
  91 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain M residue    3 GLN
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain H residue  197 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 94 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0970
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.143667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.104513 restraints weight = 13438.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.34
r_work: 0.3255 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8509  Z= 0.149
  Angle     :  0.669  17.389  11594  Z= 0.346
  Chirality :  0.046   0.271   1298
  Planarity :  0.005   0.078   1487
  Dihedral  :  4.923  48.512   1209
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.48 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.26), residues: 1072
  helix: -2.56 (0.59), residues: 51
  sheet:  1.49 (0.25), residues: 451
  loop : -0.76 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  78 
 TYR   0.014   0.002   TYR H 109 
 PHE   0.011   0.001   PHE L 119 
 TRP   0.007   0.001   TRP N 150 
 HIS   0.009   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8493)
  covalent geometry    : angle       0.65688 (11560)
  SS BOND              : bond        0.00746 (   14)
  SS BOND              : angle       2.63969 (   28)
  hydrogen bonds       : bond        0.03796 (  317)
  hydrogen bonds       : angle       5.38927 (  891)
  link_BETA1-4         : bond        0.00269 (    1)
  link_BETA1-4         : angle       1.44802 (    3)
  link_NAG-ASN         : bond        0.00057 (    1)
  link_NAG-ASN         : angle       1.11822 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8348 (m) cc_final: 0.8115 (p)
REVERT: M   75 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8672 (mttp)
REVERT: M  215 LYS cc_start: 0.5352 (mmtm) cc_final: 0.4746 (tptt)
REVERT: N  191 HIS cc_start: 0.4395 (m-70) cc_final: 0.4101 (m-70)
REVERT: H  105 ASP cc_start: 0.8134 (p0) cc_final: 0.7787 (p0)
REVERT: L   78 ARG cc_start: 0.7087 (mmm160) cc_final: 0.6094 (tpt-90)
REVERT: L  166 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5310 (pp20)
REVERT: L  195 CYS cc_start: 0.4857 (OUTLIER) cc_final: 0.4625 (t)
  outliers start: 22
  outliers final: 9
  residues processed: 94
  average time/residue: 0.7531
  time to fit residues: 74.4468
Evaluate side-chains
  90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue  159 VAL
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain H residue  197 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0070
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 72 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
H  66 ASN
** L 211 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 = 0.3980 r_free = 0.3980 target = 0.145553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.106508 restraints weight = 13317.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.28
r_work: 0.3279 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8509  Z= 0.109
  Angle     :  0.614  15.452  11594  Z= 0.317
  Chirality :  0.045   0.248   1298
  Planarity :  0.005   0.074   1487
  Dihedral  :  4.603  45.758   1209
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.90 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.26), residues: 1072
  helix: -2.79 (0.56), residues: 57
  sheet:  1.55 (0.25), residues: 450
  loop : -0.62 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  78 
 TYR   0.009   0.001   TYR M 154 
 PHE   0.008   0.001   PHE N 211 
 TRP   0.009   0.001   TRP H 118 
 HIS   0.010   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8493)
  covalent geometry    : angle       0.60098 (11560)
  SS BOND              : bond        0.00521 (   14)
  SS BOND              : angle       2.55126 (   28)
  hydrogen bonds       : bond        0.03283 (  317)
  hydrogen bonds       : angle       5.20404 (  891)
  link_BETA1-4         : bond        0.00271 (    1)
  link_BETA1-4         : angle       1.37161 (    3)
  link_NAG-ASN         : bond        0.00128 (    1)
  link_NAG-ASN         : angle       1.00969 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8345 (m) cc_final: 0.8116 (p)
REVERT: M   75 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8677 (mttp)
REVERT: M  215 LYS cc_start: 0.5289 (mmtm) cc_final: 0.4748 (tptt)
REVERT: N  191 HIS cc_start: 0.4229 (m-70) cc_final: 0.3993 (m-70)
REVERT: L   78 ARG cc_start: 0.7049 (mmm160) cc_final: 0.6059 (tpt-90)
REVERT: L  166 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5541 (pp20)
REVERT: L  195 CYS cc_start: 0.4608 (OUTLIER) cc_final: 0.4289 (t)
  outliers start: 21
  outliers final: 7
  residues processed: 97
  average time/residue: 0.7432
  time to fit residues: 75.8998
Evaluate side-chains
  90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain M residue  159 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain H residue  197 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0870
   chunk 45 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0870
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.145408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.106614 restraints weight = 13208.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.32
r_work: 0.3277 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8509  Z= 0.115
  Angle     :  0.631  15.364  11594  Z= 0.326
  Chirality :  0.045   0.271   1298
  Planarity :  0.005   0.075   1487
  Dihedral  :  4.586  45.250   1209
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.87 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.26), residues: 1072
  helix: -3.00 (0.58), residues: 51
  sheet:  1.67 (0.26), residues: 431
  loop : -0.64 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  78 
 TYR   0.011   0.001   TYR H  96 
 PHE   0.008   0.001   PHE N 211 
 TRP   0.007   0.001   TRP H 118 
 HIS   0.010   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8493)
  covalent geometry    : angle       0.61741 (11560)
  SS BOND              : bond        0.00651 (   14)
  SS BOND              : angle       2.68259 (   28)
  hydrogen bonds       : bond        0.03350 (  317)
  hydrogen bonds       : angle       5.15845 (  891)
  link_BETA1-4         : bond        0.00292 (    1)
  link_BETA1-4         : angle       1.30537 (    3)
  link_NAG-ASN         : bond        0.00113 (    1)
  link_NAG-ASN         : angle       1.03256 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8374 (m) cc_final: 0.8106 (p)
REVERT: M   43 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8916 (mmmt)
REVERT: M   75 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8676 (mttp)
REVERT: M  215 LYS cc_start: 0.5247 (mmtm) cc_final: 0.4742 (tptt)
REVERT: L   78 ARG cc_start: 0.7137 (mmm160) cc_final: 0.6483 (tmt170)
REVERT: L  166 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5484 (pp20)
REVERT: L  195 CYS cc_start: 0.4604 (OUTLIER) cc_final: 0.4268 (t)
  outliers start: 17
  outliers final: 7
  residues processed: 93
  average time/residue: 0.8223
  time to fit residues: 79.9817
Evaluate side-chains
  88 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue   98 GLU
Chi-restraints excluded: chain M residue  159 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain H residue  197 VAL
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0870
   chunk 102 optimal weight:    4.9990
   chunk 18 optimal weight:    0.2980
   chunk 71 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
N 191 HIS
L 200 GLN
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.145265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.106604 restraints weight = 13276.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.30
r_work: 0.3270 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8509  Z= 0.119
  Angle     :  0.636  16.582  11594  Z= 0.328
  Chirality :  0.045   0.256   1298
  Planarity :  0.005   0.074   1487
  Dihedral  :  4.628  44.933   1209
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.19 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.26), residues: 1072
  helix: -3.02 (0.57), residues: 51
  sheet:  1.67 (0.26), residues: 431
  loop : -0.64 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 408 
 TYR   0.011   0.001   TYR H  96 
 PHE   0.009   0.001   PHE N 211 
 TRP   0.007   0.001   TRP H 118 
 HIS   0.010   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8493)
  covalent geometry    : angle       0.62153 (11560)
  SS BOND              : bond        0.00666 (   14)
  SS BOND              : angle       2.79049 (   28)
  hydrogen bonds       : bond        0.03365 (  317)
  hydrogen bonds       : angle       5.15708 (  891)
  link_BETA1-4         : bond        0.00295 (    1)
  link_BETA1-4         : angle       1.26462 (    3)
  link_NAG-ASN         : bond        0.00102 (    1)
  link_NAG-ASN         : angle       1.03391 (    3)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 SER cc_start: 0.8363 (m) cc_final: 0.8109 (p)
REVERT: M   43 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8910 (mmmt)
REVERT: M   75 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8678 (mttp)
REVERT: M  215 LYS cc_start: 0.5279 (mmtm) cc_final: 0.4786 (tptt)
REVERT: L   78 ARG cc_start: 0.7149 (mmm160) cc_final: 0.6503 (tmt170)
REVERT: L  166 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5524 (pp20)
REVERT: L  195 CYS cc_start: 0.4638 (OUTLIER) cc_final: 0.4318 (t)
  outliers start: 14
  outliers final: 7
  residues processed: 91
  average time/residue: 0.8216
  time to fit residues: 78.3882
Evaluate side-chains
  89 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain M residue   75 LYS
Chi-restraints excluded: chain M residue  159 VAL
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue  127 LEU
Chi-restraints excluded: chain N residue  177 LEU
Chi-restraints excluded: chain H residue  197 VAL
Chi-restraints excluded: chain L residue  135 CYS
Chi-restraints excluded: chain L residue  166 GLU
Chi-restraints excluded: chain L residue  195 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 92 optimal weight:    0.5980
   chunk 53 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0270
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 519 HIS
H 214 ASN
L 200 GLN
** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.145613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.106832 restraints weight = 13272.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.34
r_work: 0.3276 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8509  Z= 0.116
  Angle     :  0.634  15.614  11594  Z= 0.327
  Chirality :  0.045   0.235   1298
  Planarity :  0.005   0.073   1487
  Dihedral  :  4.581  43.787   1209
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 15.29 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.61 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.26), residues: 1072
  helix: -2.99 (0.57), residues: 51
  sheet:  1.67 (0.26), residues: 431
  loop : -0.62 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG N  18 
 TYR   0.011   0.001   TYR H  96 
 PHE   0.008   0.001   PHE N 211 
 TRP   0.007   0.001   TRP H 118 
 HIS   0.010   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8493)
  covalent geometry    : angle       0.62010 (11560)
  SS BOND              : bond        0.00598 (   14)
  SS BOND              : angle       2.71292 (   28)
  hydrogen bonds       : bond        0.03304 (  317)
  hydrogen bonds       : angle       5.14013 (  891)
  link_BETA1-4         : bond        0.00277 (    1)
  link_BETA1-4         : angle       1.21758 (    3)
  link_NAG-ASN         : bond        0.00105 (    1)
  link_NAG-ASN         : angle       1.01788 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3961.63 seconds
wall clock time: 68 minutes 12.12 seconds (4092.12 seconds total)