Starting phenix.real_space_refine
on Wed Sep 17 06:35:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gml_51450/09_2025/9gml_51450.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gml_51450/09_2025/9gml_51450.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gml_51450/09_2025/9gml_51450.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gml_51450/09_2025/9gml_51450.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gml_51450/09_2025/9gml_51450.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gml_51450/09_2025/9gml_51450.cif"
  }
  resolution = 3.12
  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=   0.005 sd=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ni      2      6.56       5
     S      30      5.16       5
     C    3788      2.51       5
     N    1046      2.21       5
     O    1186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 6052
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 777
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'CXM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 952
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
    Chain: "C"
      Number of atoms: 4318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4318
          Classifications: {'peptide': 570}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 541}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' NI': 2, ' OH': 1}
          Classifications: {'undetermined': 3, 'water': 2}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 16
    residue:
      pdb=" N   GLN A  12 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NE2 GLN A  12 " occ=0.50
    residue:
      pdb=" N   ARG A  66 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG A  66 " occ=0.50
    residue:
      pdb=" N   ASP A  67 " occ=0.50
      ... (6 atoms not shown)
      pdb=" OD2 ASP A  67 " occ=0.50
    residue:
      pdb=" N   ASP A  79 " occ=0.50
      ... (6 atoms not shown)
      pdb=" OD2 ASP A  79 " occ=0.50
    residue:
      pdb=" N   SER B  33 " occ=0.70
      ... (4 atoms not shown)
      pdb=" OG  SER B  33 " occ=0.70
    residue:
      pdb=" N   GLU B  54 " occ=0.70
      ... (7 atoms not shown)
      pdb=" OE2 GLU B  54 " occ=0.70
    residue:
      pdb=" N   GLU B 111 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 111 " occ=0.50
    residue:
      pdb=" N   ARG C   5 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG C   5 " occ=0.50
    residue:
      pdb=" N   ASP C  26 " occ=0.50
      ... (6 atoms not shown)
      pdb=" OD2 ASP C  26 " occ=0.50
    residue:
      pdb=" N   LYS C  48 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS C  48 " occ=0.50
    residue:
      pdb=" N   LYS C 185 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS C 185 " occ=0.50
    residue:
      pdb=" N   MET C 360 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET C 360 " occ=0.50
    ... (remaining 4 not shown)
  Time building chain proxies: 1.63, per 1000 atoms: 0.27
  Number of scatterers: 6052
  At special positions: 0
  Unit cell: (114.24, 81.6, 81.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ni      2     28.00
     S      30     16.00
     O    1186      8.00
     N    1046      7.00
     C    3788      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 290.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1416

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      33.8% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 27
      removed outlier: 3.634A  pdb=" N   LYS A   8 " --> pdb=" O   ASN A   4 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLN A  12 " --> pdb=" O   LYS A   8 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE A  13 " --> pdb=" O   GLU A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 50
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 61 through 63
      No H-bonds generated for 'chain 'A' and resid 61 through 63'
    Processing helix  chain 'A' and resid 72 through 76
    Processing helix  chain 'B' and resid 109 through 120
      removed outlier: 3.647A  pdb=" N   ILE B 113 " --> pdb=" O   ASN B 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 12
    Processing helix  chain 'C' and resid 144 through 151
      removed outlier: 3.996A  pdb=" N   VAL C 148 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 171
    Processing helix  chain 'C' and resid 175 through 187
      removed outlier: 4.158A  pdb=" N   ASN C 179 " --> pdb=" O   PRO C 175 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 190
      No H-bonds generated for 'chain 'C' and resid 188 through 190'
    Processing helix  chain 'C' and resid 204 through 213
      removed outlier: 3.983A  pdb=" N   ILE C 208 " --> pdb=" O   SER C 204 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLN C 211 " --> pdb=" O   PRO C 207 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE C 212 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 226
    Processing helix  chain 'C' and resid 228 through 243
    Processing helix  chain 'C' and resid 258 through 267
      removed outlier: 3.659A  pdb=" N   THR C 262 " --> pdb=" O   PHE C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 285 through 293
      removed outlier: 4.529A  pdb=" N   MET C 288 " --> pdb=" O   PRO C 285 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA C 289 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   HIS C 293 " --> pdb=" O   MET C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 323
      removed outlier: 3.547A  pdb=" N   GLU C 314 " --> pdb=" O   ASN C 310 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   HIS C 323 " --> pdb=" O   LEU C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 340
      removed outlier: 3.864A  pdb=" N   VAL C 333 " --> pdb=" O   ILE C 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 354
      removed outlier: 3.559A  pdb=" N   ILE C 345 " --> pdb=" O   ARG C 341 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ILE C 350 " --> pdb=" O   ALA C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 369 through 371
      No H-bonds generated for 'chain 'C' and resid 369 through 371'
    Processing helix  chain 'C' and resid 372 through 389
    Processing helix  chain 'C' and resid 399 through 408
    Processing helix  chain 'C' and resid 412 through 419
    Processing helix  chain 'C' and resid 439 through 443
      removed outlier: 3.650A  pdb=" N   PHE C 443 " --> pdb=" O   PRO C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 483
      removed outlier: 3.571A  pdb=" N   VAL C 483 " --> pdb=" O   TYR C 480 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 480 through 483'
    Processing helix  chain 'C' and resid 485 through 489
    Processing helix  chain 'C' and resid 497 through 502
    Processing helix  chain 'C' and resid 503 through 509
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 86
    Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 20
    Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56
    Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 42
    Processing sheet with id=AA5, first strand: chain 'B' and resid 95 through 96
    Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 21
    Processing sheet with id=AA7, first strand: chain 'C' and resid 33 through 34
      removed outlier: 7.111A  pdb=" N   LYS C  33 " --> pdb=" O   LYS C  84 " (cutoff:3.500A)
      removed outlier: 9.556A  pdb=" N   ASP C  86 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ILE C  87 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   THR C  72 " --> pdb=" O   ILE C  87 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   VAL C  89 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   LEU C  70 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LEU C  70 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 98
      removed outlier: 5.217A  pdb=" N   ILE C  94 " --> pdb=" O   LYS C  90 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LYS C  90 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ILE C  87 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   THR C  72 " --> pdb=" O   ILE C  87 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   VAL C  89 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   LEU C  70 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   VAL C 129 " --> pdb=" O   ASN C  73 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   LEU C  75 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   ALA C 131 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
      removed outlier: 9.119A  pdb=" N   LEU C  77 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   LYS C 452 " --> pdb=" O   ILE C 456 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   ILE C 456 " --> pdb=" O   LYS C 452 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 133 through 139
      removed outlier: 5.870A  pdb=" N   GLY C 133 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR C 156 " --> pdb=" O   GLY C 133 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   HIS C 137 " --> pdb=" O   PHE C 158 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   GLY C 160 " --> pdb=" O   HIS C 137 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   HIS C 139 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY C 218 " --> pdb=" O   ILE C 196 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   LEU C 219 " --> pdb=" O   ALA C 247 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   VAL C 246 " --> pdb=" O   HIS C 272 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 492 through 496
      removed outlier: 6.403A  pdb=" N   THR C 493 " --> pdb=" O   GLY C 515 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   VAL C 517 " --> pdb=" O   THR C 493 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   MET C 495 " --> pdb=" O   VAL C 517 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 538 through 539

    216 hydrogen bonds defined for protein.
    585 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: 0.84

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2063
        1.34 -     1.46: 1131
        1.46 -     1.58: 2901
        1.58 -     1.70: 0
        1.70 -     1.82: 57
  Bond restraints: 6152
  Sorted by residual:
  bond pdb=" NZ  KCX C 220 "
       pdb=" CX  KCX C 220 "
    ideal  model  delta    sigma   weight residual
    1.411  1.331  0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" CE  KCX C 220 "
       pdb=" NZ  KCX C 220 "
    ideal  model  delta    sigma   weight residual
    1.442  1.489 -0.047 2.00e-02 2.50e+03 5.48e+00
  bond pdb=" SD  CXM A   1 "
       pdb=" CE  CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.808  1.764  0.044 2.00e-02 2.50e+03 4.91e+00
  bond pdb=" C   CXM A   1 "
       pdb=" O   CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.231  1.268 -0.037 2.00e-02 2.50e+03 3.49e+00
  bond pdb=" CA  CXM A   1 "
       pdb=" C   CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.561 -0.036 2.10e-02 2.27e+03 3.01e+00
  ... (remaining 6147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 8159
        2.12 -     4.25: 133
        4.25 -     6.37: 28
        6.37 -     8.49: 6
        8.49 -    10.61: 2
  Bond angle restraints: 8328
  Sorted by residual:
  angle pdb=" N   VAL B  49 "
        pdb=" CA  VAL B  49 "
        pdb=" C   VAL B  49 "
      ideal   model   delta    sigma   weight residual
     112.96  108.33    4.63 1.00e+00 1.00e+00 2.14e+01
  angle pdb=" CB  LYS C   2 "
        pdb=" CG  LYS C   2 "
        pdb=" CD  LYS C   2 "
      ideal   model   delta    sigma   weight residual
     111.30  121.91  -10.61 2.30e+00 1.89e-01 2.13e+01
  angle pdb=" C   ALA C  23 "
        pdb=" CA  ALA C  23 "
        pdb=" CB  ALA C  23 "
      ideal   model   delta    sigma   weight residual
     115.89  110.54    5.35 1.32e+00 5.74e-01 1.64e+01
  angle pdb=" CA  LYS B 118 "
        pdb=" CB  LYS B 118 "
        pdb=" CG  LYS B 118 "
      ideal   model   delta    sigma   weight residual
     114.10  121.39   -7.29 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" N   THR C 470 "
        pdb=" CA  THR C 470 "
        pdb=" C   THR C 470 "
      ideal   model   delta    sigma   weight residual
     109.81  117.43   -7.62 2.21e+00 2.05e-01 1.19e+01
  ... (remaining 8323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.10: 3124
       18.10 -    36.19: 456
       36.19 -    54.29: 105
       54.29 -    72.38: 13
       72.38 -    90.48: 14
  Dihedral angle restraints: 3712
    sinusoidal: 1489
      harmonic: 2223
  Sorted by residual:
  dihedral pdb=" CA  MET C 563 "
           pdb=" C   MET C 563 "
           pdb=" N   ALA C 564 "
           pdb=" CA  ALA C 564 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.00  -26.00     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  TRP C 438 "
           pdb=" C   TRP C 438 "
           pdb=" N   GLU C 439 "
           pdb=" CA  GLU C 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.28   16.72     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CB  GLU A  83 "
           pdb=" CG  GLU A  83 "
           pdb=" CD  GLU A  83 "
           pdb=" OE1 GLU A  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   90.48  -90.48     1      3.00e+01 1.11e-03 1.08e+01
  ... (remaining 3709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 598
       0.036 -    0.073: 212
       0.073 -    0.109: 100
       0.109 -    0.145: 26
       0.145 -    0.181: 5
  Chirality restraints: 941
  Sorted by residual:
  chirality pdb=" CA  ILE C  97 "
            pdb=" N   ILE C  97 "
            pdb=" C   ILE C  97 "
            pdb=" CB  ILE C  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.23e-01
  chirality pdb=" CA  THR C 470 "
            pdb=" N   THR C 470 "
            pdb=" C   THR C 470 "
            pdb=" CB  THR C 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 8.04e-01
  chirality pdb=" CA  ASN C 302 "
            pdb=" N   ASN C 302 "
            pdb=" C   ASN C 302 "
            pdb=" CB  ASN C 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.23e-01
  ... (remaining 938 not shown)

  Planarity restraints: 1100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 302 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO C 303 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO C 303 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 303 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C  26 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.85e+00
        pdb=" C   ASP C  26 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ASP C  26 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU C  27 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C  26 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.10e+00
        pdb=" CG  ASP C  26 "   -0.035 2.00e-02 2.50e+03
        pdb=" OD1 ASP C  26 "    0.013 2.00e-02 2.50e+03
        pdb=" OD2 ASP C  26 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1097 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 69
        2.54 -     3.13: 4787
        3.13 -     3.72: 9497
        3.72 -     4.31: 12744
        4.31 -     4.90: 21826
  Nonbonded interactions: 48923
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS C 137 "
            pdb="NI    NI C 602 "
     model   vdw
     1.950 2.260
  nonbonded pdb=" NE2 HIS C 275 "
            pdb="NI    NI C 601 "
     model   vdw
     1.963 2.260
  nonbonded pdb="NI    NI C 602 "
            pdb=" O    OH C 603 "
     model   vdw
     1.969 2.180
  nonbonded pdb="NI    NI C 601 "
            pdb=" O    OH C 603 "
     model   vdw
     1.975 2.180
  nonbonded pdb=" OQ1 KCX C 220 "
            pdb="NI    NI C 601 "
     model   vdw
     1.976 2.180
  ... (remaining 48918 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=0.50 max=1.00 mean=0.98
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:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     6.920
  Find NCS groups from input model:        0.030
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   6152  Z= 0.166
  Angle     :  0.693  10.614   8328  Z= 0.364
  Chirality :  0.048   0.181    941
  Planarity :  0.004   0.057   1100
  Dihedral  : 17.847  90.481   2296
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 34.58 %
    Favored  : 65.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.23 (0.30), residues: 782
  helix:  0.72 (0.35), residues: 231
  sheet:  1.11 (0.55), residues: 94
  loop : -0.91 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 341 
 TYR   0.010   0.001   TYR C  12 
 PHE   0.006   0.001   PHE C 443 
 TRP   0.016   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6152)
  covalent geometry    : angle       0.69286 ( 8328)
  hydrogen bonds       : bond        0.13343 (  210)
  hydrogen bonds       : angle       6.41445 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 212
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.9027 (mmmt) cc_final: 0.8440 (pttt)
REVERT: A   34 GLU cc_start: 0.8260 (pm20) cc_final: 0.7963 (pm20)
REVERT: C   43 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8354 (p0)
REVERT: C  223 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7663 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0769
  time to fit residues: 21.4186
Evaluate side-chains
  197 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0970
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B   5 ASN
** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 400 ASN
C 488 HIS
** C 491 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 = 0.3684 r_free = 0.3684 target = 0.107338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.095114 restraints weight = 13956.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 3.07
r_work: 0.3362 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3312
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6152  Z= 0.118
  Angle     :  0.611   7.743   8328  Z= 0.312
  Chirality :  0.047   0.188    941
  Planarity :  0.004   0.055   1100
  Dihedral  :  4.853  51.488    855
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.84 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 30.06 %
    Favored  : 65.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.18 (0.30), residues: 782
  helix:  0.93 (0.35), residues: 233
  sheet:  0.88 (0.58), residues: 87
  loop : -0.90 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 264 
 TYR   0.016   0.001   TYR A  32 
 PHE   0.012   0.001   PHE A  14 
 TRP   0.013   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6152)
  covalent geometry    : angle       0.61081 ( 8328)
  hydrogen bonds       : bond        0.03448 (  210)
  hydrogen bonds       : angle       4.91161 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8621 (mtmm)
REVERT: A   10 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8374 (pttt)
REVERT: A   49 ASP cc_start: 0.8751 (m-30) cc_final: 0.8477 (t0)
REVERT: A   51 LYS cc_start: 0.9125 (mptp) cc_final: 0.8924 (mptp)
REVERT: C   43 ASN cc_start: 0.8658 (p0) cc_final: 0.8205 (p0)
REVERT: C  166 GLU cc_start: 0.2320 (mp0) cc_final: 0.1933 (mp0)
REVERT: C  446 LYS cc_start: 0.5617 (mtpt) cc_final: 0.5358 (mtmt)
REVERT: C  511 LYS cc_start: 0.9081 (mttp) cc_final: 0.8843 (mtmm)
  outliers start: 27
  outliers final: 18
  residues processed: 208
  average time/residue: 0.0742
  time to fit residues: 20.4841
Evaluate side-chains
  212 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 194
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  510 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0870
   chunk 23 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    3.4166

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
B   5 ASN
C 283 HIS
C 418 GLN
** C 491 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 = 0.3568 r_free = 0.3568 target = 0.099899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.087469 restraints weight = 13945.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 3.05
r_work: 0.3214 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   6152  Z= 0.270
  Angle     :  0.676   7.662   8328  Z= 0.351
  Chirality :  0.050   0.199    941
  Planarity :  0.005   0.059   1100
  Dihedral  :  5.114  46.024    853
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.86 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 29.13 %
    Favored  : 64.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.40 (0.30), residues: 782
  helix:  0.78 (0.34), residues: 232
  sheet:  0.77 (0.58), residues: 90
  loop : -1.06 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 264 
 TYR   0.013   0.002   TYR A  32 
 PHE   0.015   0.002   PHE A  14 
 TRP   0.015   0.002   TRP C 438 
 HIS   0.004   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 ( 6152)
  covalent geometry    : angle       0.67614 ( 8328)
  hydrogen bonds       : bond        0.04657 (  210)
  hydrogen bonds       : angle       4.91854 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 198
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8346 (pttt)
REVERT: A   34 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8226 (pm20)
REVERT: B   31 ARG cc_start: 0.8963 (tpp80) cc_final: 0.8645 (ttm-80)
REVERT: B   34 ASN cc_start: 0.9202 (t0) cc_final: 0.8983 (t0)
REVERT: B   52 ASN cc_start: 0.7083 (t0) cc_final: 0.6218 (t0)
REVERT: C   43 ASN cc_start: 0.8592 (p0) cc_final: 0.8162 (p0)
REVERT: C  166 GLU cc_start: 0.2351 (mp0) cc_final: 0.1004 (mp0)
REVERT: C  181 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8539 (mm-30)
REVERT: C  185 LYS cc_start: 0.4788 (tmtt) cc_final: 0.3947 (tmtt)
REVERT: C  341 ARG cc_start: 0.8360 (ptt-90) cc_final: 0.7695 (ptp-170)
  outliers start: 42
  outliers final: 32
  residues processed: 217
  average time/residue: 0.0676
  time to fit residues: 19.6818
Evaluate side-chains
  225 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 192
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  394 GLU
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  510 LEU
Chi-restraints excluded: chain C residue  543 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
B   5 ASN
B  68 ASN
** C 491 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 = 0.3595 r_free = 0.3595 target = 0.102711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.090099 restraints weight = 13723.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.08
r_work: 0.3241 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3246
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6152  Z= 0.158
  Angle     :  0.628  12.113   8328  Z= 0.320
  Chirality :  0.048   0.201    941
  Planarity :  0.004   0.058   1100
  Dihedral  :  5.003  49.111    853
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.35 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 31.15 %
    Favored  : 63.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.38 (0.30), residues: 782
  helix:  0.87 (0.34), residues: 233
  sheet:  0.72 (0.58), residues: 90
  loop : -1.08 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 264 
 TYR   0.018   0.001   TYR A  32 
 PHE   0.016   0.001   PHE A  14 
 TRP   0.016   0.001   TRP C 438 
 HIS   0.002   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6152)
  covalent geometry    : angle       0.62776 ( 8328)
  hydrogen bonds       : bond        0.03845 (  210)
  hydrogen bonds       : angle       4.71394 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 198
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.9297 (mmmt) cc_final: 0.8315 (pttt)
REVERT: A   34 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8143 (pm20)
REVERT: B   31 ARG cc_start: 0.8795 (tpp80) cc_final: 0.8540 (ttm-80)
REVERT: B   52 ASN cc_start: 0.7138 (t0) cc_final: 0.6263 (t0)
REVERT: C   43 ASN cc_start: 0.8584 (p0) cc_final: 0.8132 (p0)
REVERT: C  166 GLU cc_start: 0.2099 (mp0) cc_final: 0.0312 (mp0)
REVERT: C  181 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8445 (mm-30)
REVERT: C  185 LYS cc_start: 0.4317 (tmtt) cc_final: 0.3487 (tmtt)
REVERT: C  485 ASP cc_start: 0.7872 (p0) cc_final: 0.7640 (p0)
  outliers start: 34
  outliers final: 28
  residues processed: 211
  average time/residue: 0.0704
  time to fit residues: 19.5145
Evaluate side-chains
  223 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 194
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  510 LEU
Chi-restraints excluded: chain C residue  543 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C 418 GLN
** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.099495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.087071 restraints weight = 13808.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.13
r_work: 0.3267 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6152  Z= 0.123
  Angle     :  0.611   9.520   8328  Z= 0.310
  Chirality :  0.048   0.202    941
  Planarity :  0.004   0.057   1100
  Dihedral  :  4.789  47.923    853
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.09 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 31.62 %
    Favored  : 62.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.27 (0.30), residues: 782
  helix:  0.98 (0.35), residues: 233
  sheet:  0.74 (0.58), residues: 89
  loop : -1.01 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 264 
 TYR   0.014   0.001   TYR A  32 
 PHE   0.014   0.001   PHE B  97 
 TRP   0.016   0.001   TRP C 438 
 HIS   0.004   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6152)
  covalent geometry    : angle       0.61125 ( 8328)
  hydrogen bonds       : bond        0.03399 (  210)
  hydrogen bonds       : angle       4.56779 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 193
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.9278 (mmmt) cc_final: 0.8240 (tttt)
REVERT: B   27 LYS cc_start: 0.9008 (mtpp) cc_final: 0.8685 (mtpp)
REVERT: B   31 ARG cc_start: 0.8769 (tpp80) cc_final: 0.8464 (ttm-80)
REVERT: B   52 ASN cc_start: 0.7059 (t0) cc_final: 0.6182 (t0)
REVERT: C   43 ASN cc_start: 0.8569 (p0) cc_final: 0.8133 (p0)
REVERT: C  147 ASP cc_start: 0.8751 (m-30) cc_final: 0.8526 (m-30)
REVERT: C  158 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8595 (m-80)
REVERT: C  166 GLU cc_start: 0.2152 (mp0) cc_final: 0.1292 (mp0)
REVERT: C  185 LYS cc_start: 0.4538 (tmtt) cc_final: 0.4005 (tmtt)
REVERT: C  485 ASP cc_start: 0.7861 (p0) cc_final: 0.7649 (p0)
REVERT: C  545 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8107 (tm-30)
  outliers start: 37
  outliers final: 28
  residues processed: 212
  average time/residue: 0.0604
  time to fit residues: 17.2256
Evaluate side-chains
  221 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 191
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  394 GLU
Chi-restraints excluded: chain C residue  465 SER
Chi-restraints excluded: chain C residue  510 LEU
Chi-restraints excluded: chain C residue  543 THR
Chi-restraints excluded: chain C residue  545 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 78 optimal weight:    0.1980
   chunk 7 optimal weight:    0.0170
   chunk 28 optimal weight:    0.0050
   chunk 73 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   overall best weight:    1.0436

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

Flipped N/Q/H residues before XYZ refinement:
** C 491 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 = 0.3606 r_free = 0.3606 target = 0.099347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.086972 restraints weight = 13625.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.12
r_work: 0.3268 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6152  Z= 0.121
  Angle     :  0.617  13.068   8328  Z= 0.309
  Chirality :  0.047   0.198    941
  Planarity :  0.004   0.057   1100
  Dihedral  :  4.671  45.501    853
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.48 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  6.23 %
    Allowed  : 32.40 %
    Favored  : 61.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.22 (0.30), residues: 782
  helix:  0.99 (0.35), residues: 233
  sheet:  0.79 (0.58), residues: 89
  loop : -0.97 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 264 
 TYR   0.011   0.001   TYR A  32 
 PHE   0.020   0.001   PHE A  14 
 TRP   0.016   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6152)
  covalent geometry    : angle       0.61673 ( 8328)
  hydrogen bonds       : bond        0.03279 (  210)
  hydrogen bonds       : angle       4.51961 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 194
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.9282 (mmmt) cc_final: 0.8251 (tttt)
REVERT: A   34 GLU cc_start: 0.8366 (pm20) cc_final: 0.7860 (pm20)
REVERT: B   27 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8762 (mtpp)
REVERT: B   31 ARG cc_start: 0.8775 (tpp80) cc_final: 0.8457 (ttm-80)
REVERT: B   52 ASN cc_start: 0.7069 (t0) cc_final: 0.6174 (t0)
REVERT: B   95 GLU cc_start: 0.7916 (mp0) cc_final: 0.7650 (mp0)
REVERT: C   32 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8088 (mt-10)
REVERT: C   43 ASN cc_start: 0.8563 (p0) cc_final: 0.8126 (p0)
REVERT: C  144 ASP cc_start: 0.8752 (m-30) cc_final: 0.8429 (m-30)
REVERT: C  147 ASP cc_start: 0.8750 (m-30) cc_final: 0.8520 (m-30)
REVERT: C  158 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8616 (m-80)
REVERT: C  166 GLU cc_start: 0.2193 (mp0) cc_final: 0.0235 (mp0)
REVERT: C  185 LYS cc_start: 0.4528 (tmtt) cc_final: 0.3964 (tmtt)
REVERT: C  545 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8100 (tm-30)
  outliers start: 40
  outliers final: 30
  residues processed: 218
  average time/residue: 0.0717
  time to fit residues: 20.8727
Evaluate side-chains
  224 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 191
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   32 GLU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  172 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  394 GLU
Chi-restraints excluded: chain C residue  424 VAL
Chi-restraints excluded: chain C residue  543 THR
Chi-restraints excluded: chain C residue  545 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0370
   chunk 56 optimal weight:    5.9990
   chunk 22 optimal weight:    0.4980
   chunk 73 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0870
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
C 418 GLN
** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.101057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.088930 restraints weight = 13712.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 3.03
r_work: 0.3314 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3312
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3312
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6152  Z= 0.108
  Angle     :  0.620  13.117   8328  Z= 0.309
  Chirality :  0.047   0.200    941
  Planarity :  0.004   0.055   1100
  Dihedral  :  4.458  43.279    853
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.45 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 33.64 %
    Favored  : 61.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.14 (0.30), residues: 782
  helix:  1.11 (0.35), residues: 233
  sheet:  0.75 (0.59), residues: 89
  loop : -0.93 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 264 
 TYR   0.010   0.001   TYR A  32 
 PHE   0.015   0.001   PHE B  97 
 TRP   0.016   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6152)
  covalent geometry    : angle       0.62010 ( 8328)
  hydrogen bonds       : bond        0.02820 (  210)
  hydrogen bonds       : angle       4.39606 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 197
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8274 (tttt)
REVERT: B   27 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8724 (mtpp)
REVERT: B   31 ARG cc_start: 0.8734 (tpp80) cc_final: 0.8486 (ttm-80)
REVERT: C   43 ASN cc_start: 0.8541 (p0) cc_final: 0.8112 (p0)
REVERT: C  144 ASP cc_start: 0.8715 (m-30) cc_final: 0.8444 (m-30)
REVERT: C  158 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8534 (m-80)
REVERT: C  166 GLU cc_start: 0.2158 (mp0) cc_final: 0.1142 (mp0)
REVERT: C  185 LYS cc_start: 0.4416 (tmtt) cc_final: 0.3906 (tmtt)
REVERT: C  439 GLU cc_start: 0.8660 (mp0) cc_final: 0.8270 (mp0)
REVERT: C  511 LYS cc_start: 0.9028 (mttp) cc_final: 0.8792 (mtmm)
  outliers start: 34
  outliers final: 23
  residues processed: 219
  average time/residue: 0.0691
  time to fit residues: 20.2954
Evaluate side-chains
  215 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  172 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  424 VAL
Chi-restraints excluded: chain C residue  465 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 379 GLN
** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.098562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.086284 restraints weight = 13832.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 3.08
r_work: 0.3236 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6152  Z= 0.200
  Angle     :  0.683  12.302   8328  Z= 0.344
  Chirality :  0.049   0.198    941
  Planarity :  0.005   0.059   1100
  Dihedral  :  4.723  38.095    853
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.99 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 31.93 %
    Favored  : 62.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.19 (0.30), residues: 782
  helix:  1.08 (0.35), residues: 233
  sheet:  0.96 (0.60), residues: 86
  loop : -1.01 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  21 
 TYR   0.009   0.001   TYR B  12 
 PHE   0.023   0.001   PHE A  14 
 TRP   0.014   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 6152)
  covalent geometry    : angle       0.68331 ( 8328)
  hydrogen bonds       : bond        0.03973 (  210)
  hydrogen bonds       : angle       4.60392 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 195
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8321 (tttt)
REVERT: A   34 GLU cc_start: 0.8461 (pm20) cc_final: 0.7929 (pm20)
REVERT: B   31 ARG cc_start: 0.8780 (tpp80) cc_final: 0.8481 (ttm-80)
REVERT: B   52 ASN cc_start: 0.7096 (t0) cc_final: 0.6239 (t0)
REVERT: B   95 GLU cc_start: 0.7872 (mp0) cc_final: 0.7572 (mp0)
REVERT: C   32 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8088 (mt-10)
REVERT: C   43 ASN cc_start: 0.8542 (p0) cc_final: 0.8096 (p0)
REVERT: C  158 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8677 (m-80)
REVERT: C  166 GLU cc_start: 0.2120 (mp0) cc_final: 0.0377 (mp0)
REVERT: C  185 LYS cc_start: 0.4351 (tmtt) cc_final: 0.3805 (tmtt)
REVERT: C  196 ILE cc_start: 0.8184 (mm) cc_final: 0.7907 (mm)
REVERT: C  495 MET cc_start: 0.9316 (mtp) cc_final: 0.9092 (mtp)
REVERT: C  545 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8167 (tm-30)
  outliers start: 33
  outliers final: 24
  residues processed: 213
  average time/residue: 0.0733
  time to fit residues: 20.8221
Evaluate side-chains
  218 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   32 GLU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  394 GLU
Chi-restraints excluded: chain C residue  424 VAL
Chi-restraints excluded: chain C residue  465 SER
Chi-restraints excluded: chain C residue  543 THR
Chi-restraints excluded: chain C residue  545 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 418 GLN
** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.100496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.088299 restraints weight = 13821.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 3.09
r_work: 0.3274 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6152  Z= 0.130
  Angle     :  0.658  10.412   8328  Z= 0.329
  Chirality :  0.048   0.202    941
  Planarity :  0.004   0.057   1100
  Dihedral  :  4.604  39.840    853
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 32.87 %
    Favored  : 62.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.11 (0.30), residues: 782
  helix:  1.19 (0.35), residues: 233
  sheet:  0.84 (0.60), residues: 86
  loop : -0.94 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  21 
 TYR   0.008   0.001   TYR A  32 
 PHE   0.014   0.001   PHE B  97 
 TRP   0.017   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6152)
  covalent geometry    : angle       0.65754 ( 8328)
  hydrogen bonds       : bond        0.03310 (  210)
  hydrogen bonds       : angle       4.46911 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8308 (tttt)
REVERT: A   34 GLU cc_start: 0.8370 (pm20) cc_final: 0.7852 (pm20)
REVERT: B   31 ARG cc_start: 0.8741 (tpp80) cc_final: 0.8443 (ttm-80)
REVERT: B   52 ASN cc_start: 0.7090 (t0) cc_final: 0.6212 (t0)
REVERT: B   78 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8259 (pm20)
REVERT: B   95 GLU cc_start: 0.7866 (mp0) cc_final: 0.7586 (mp0)
REVERT: C   32 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8096 (mt-10)
REVERT: C   43 ASN cc_start: 0.8538 (p0) cc_final: 0.8065 (p0)
REVERT: C  158 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8630 (m-80)
REVERT: C  166 GLU cc_start: 0.2209 (mp0) cc_final: 0.0502 (mp0)
REVERT: C  185 LYS cc_start: 0.4386 (tmtt) cc_final: 0.3814 (tmtt)
REVERT: C  196 ILE cc_start: 0.8177 (mm) cc_final: 0.7907 (mm)
REVERT: C  495 MET cc_start: 0.9296 (mtp) cc_final: 0.9072 (mtp)
REVERT: C  545 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8246 (tm-30)
  outliers start: 29
  outliers final: 25
  residues processed: 214
  average time/residue: 0.0724
  time to fit residues: 20.7094
Evaluate side-chains
  223 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   32 GLU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  394 GLU
Chi-restraints excluded: chain C residue  424 VAL
Chi-restraints excluded: chain C residue  545 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 25 optimal weight:    0.1980
   chunk 62 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0070
   chunk 27 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0770
   chunk 6 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    0.8560

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.101365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.089195 restraints weight = 13622.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 3.08
r_work: 0.3292 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3301
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3301 r_free = 0.3301    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3301 r_free = 0.3301    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3301
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6152  Z= 0.125
  Angle     :  0.665   9.402   8328  Z= 0.333
  Chirality :  0.048   0.201    941
  Planarity :  0.005   0.057   1100
  Dihedral  :  4.495  37.768    853
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.48 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 33.96 %
    Favored  : 61.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.08 (0.30), residues: 782
  helix:  1.18 (0.35), residues: 234
  sheet:  0.75 (0.59), residues: 86
  loop : -0.89 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  21 
 TYR   0.010   0.001   TYR A  32 
 PHE   0.027   0.001   PHE A  14 
 TRP   0.016   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6152)
  covalent geometry    : angle       0.66508 ( 8328)
  hydrogen bonds       : bond        0.03122 (  210)
  hydrogen bonds       : angle       4.42952 (  585)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8386 (ptpp)
REVERT: A   10 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8313 (tttt)
REVERT: A   34 GLU cc_start: 0.8336 (pm20) cc_final: 0.7832 (pm20)
REVERT: A   76 MET cc_start: 0.8488 (mmt) cc_final: 0.8279 (mmp)
REVERT: B   31 ARG cc_start: 0.8726 (tpp80) cc_final: 0.8434 (ttm-80)
REVERT: B   52 ASN cc_start: 0.7083 (t0) cc_final: 0.6187 (t0)
REVERT: B   78 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8292 (pm20)
REVERT: B   95 GLU cc_start: 0.7865 (mp0) cc_final: 0.7582 (mp0)
REVERT: C   32 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8035 (mt-10)
REVERT: C  144 ASP cc_start: 0.8722 (m-30) cc_final: 0.8461 (m-30)
REVERT: C  158 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8591 (m-80)
REVERT: C  166 GLU cc_start: 0.2139 (mp0) cc_final: 0.0442 (mp0)
REVERT: C  181 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8301 (mm-30)
REVERT: C  185 LYS cc_start: 0.4199 (tmtt) cc_final: 0.3658 (tmtt)
REVERT: C  196 ILE cc_start: 0.8155 (mm) cc_final: 0.7897 (mm)
REVERT: C  439 GLU cc_start: 0.8673 (mp0) cc_final: 0.8253 (mp0)
REVERT: C  495 MET cc_start: 0.9285 (mtp) cc_final: 0.9077 (mtp)
REVERT: C  545 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8240 (tm-30)
  outliers start: 28
  outliers final: 23
  residues processed: 212
  average time/residue: 0.0662
  time to fit residues: 18.8907
Evaluate side-chains
  216 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 189
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LYS
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   18 GLU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   32 GLU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  223 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  354 LEU
Chi-restraints excluded: chain C residue  394 GLU
Chi-restraints excluded: chain C residue  424 VAL
Chi-restraints excluded: chain C residue  545 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
C 418 GLN
** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.098411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.085923 restraints weight = 13768.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.13
r_work: 0.3239 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6152  Z= 0.191
  Angle     :  0.706  11.757   8328  Z= 0.355
  Chirality :  0.050   0.288    941
  Planarity :  0.005   0.059   1100
  Dihedral  :  4.697  33.945    853
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.99 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 33.64 %
    Favored  : 61.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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: -0.15 (0.30), residues: 782
  helix:  1.13 (0.35), residues: 233
  sheet:  0.82 (0.60), residues: 86
  loop : -0.96 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  21 
 TYR   0.010   0.001   TYR A  32 
 PHE   0.012   0.001   PHE B  97 
 TRP   0.015   0.001   TRP C 438 
 HIS   0.004   0.001   HIS C 272 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6152)
  covalent geometry    : angle       0.70620 ( 8328)
  hydrogen bonds       : bond        0.03804 (  210)
  hydrogen bonds       : angle       4.57505 (  585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1503.45 seconds
wall clock time: 26 minutes 28.20 seconds (1588.20 seconds total)