Starting phenix.real_space_refine
on Wed Feb 12 03:52:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1o_36797/02_2025/8k1o_36797.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1o_36797/02_2025/8k1o_36797.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1o_36797/02_2025/8k1o_36797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1o_36797/02_2025/8k1o_36797.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1o_36797/02_2025/8k1o_36797.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1o_36797/02_2025/8k1o_36797.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.089
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: 6
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     Mg      2      5.21       5
     S      21      5.16       5
     C    4572      2.51       5
     N    1248      2.21       5
     O    1310      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7163
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 510, 3718
          Classifications: {'peptide': 510}
          Link IDs: {'PTRANS': 20, 'TRANS': 489}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1624
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 8, 'TRANS': 206}
    Chain: "C"
      Number of atoms: 1597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1597
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 8, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 160
          Unusual residues: {'CDL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 40
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.34, per 1000 atoms: 0.75
  Number of scatterers: 7163
  At special positions: 0
  Unit cell: (72.16, 110.7, 82.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      21     16.00
     P      10     15.00
     Mg      2     11.99
     O    1310      8.00
     N    1248      7.00
     C    4572      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: 1.98
  Conformation dependent library (CDL) restraints added in 909.2 milliseconds
  

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1658

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 6 sheets defined
      57.7% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 35
    Processing helix  chain 'A' and resid 40 through 48
    Processing helix  chain 'A' and resid 57 through 61
      removed outlier: 3.564A  pdb=" N   VAL A  60 " --> pdb=" O   ILE A  57 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   GLU A  61 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 57 through 61'
    Processing helix  chain 'A' and resid 66 through 76
      removed outlier: 3.534A  pdb=" N   ALA A  72 " --> pdb=" O   SER A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 87
      removed outlier: 3.520A  pdb=" N   ARG A  84 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 101
    Processing helix  chain 'A' and resid 102 through 104
      No H-bonds generated for 'chain 'A' and resid 102 through 104'
    Processing helix  chain 'A' and resid 105 through 127
      removed outlier: 3.698A  pdb=" N   LEU A 109 " --> pdb=" O   MET A 105 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A 110 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ALA A 111 " --> pdb=" O   HIS A 107 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   ASP A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
      removed outlier: 3.823A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 168
      removed outlier: 3.517A  pdb=" N   ALA A 148 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 200
      removed outlier: 3.625A  pdb=" N   SER A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 178 " --> pdb=" O   PRO A 174 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   PHE A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   THR A 192 " --> pdb=" O   GLY A 188 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA A 193 " --> pdb=" O   MET A 189 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A 194 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 195 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 228
      removed outlier: 3.587A  pdb=" N   VAL A 215 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.520A  pdb=" N   SER A 234 " --> pdb=" O   GLY A 231 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   CYS A 236 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 246
      removed outlier: 3.579A  pdb=" N   VAL A 245 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 273
      removed outlier: 3.851A  pdb=" N   LEU A 258 " --> pdb=" O   TRP A 254 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA A 263 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   TYR A 271 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 329
      removed outlier: 3.523A  pdb=" N   ASN A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   GLY A 310 " --> pdb=" O   ARG A 306 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   SER A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A 328 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   VAL A 329 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 332
      No H-bonds generated for 'chain 'A' and resid 330 through 332'
    Processing helix  chain 'A' and resid 354 through 389
      removed outlier: 3.645A  pdb=" N   GLN A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ALA A 359 " --> pdb=" O   ALA A 355 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   MET A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   LEU A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   HIS A 384 " --> pdb=" O   THR A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 397
      removed outlier: 3.548A  pdb=" N   LEU A 395 " --> pdb=" O   ARG A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 437
      removed outlier: 3.897A  pdb=" N   SER A 408 " --> pdb=" O   HIS A 404 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   HIS A 409 " --> pdb=" O   TRP A 405 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ALA A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   MET A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ALA A 418 " --> pdb=" O   LEU A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 452
      removed outlier: 3.762A  pdb=" N   VAL A 446 " --> pdb=" O   LYS A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 471
      removed outlier: 4.301A  pdb=" N   LEU A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   SER A 461 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   GLY A 469 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 476
      Proline residue:  A 476  - end of helix
    Processing helix  chain 'A' and resid 477 through 491
    Processing helix  chain 'A' and resid 520 through 542
      removed outlier: 3.744A  pdb=" N   LEU A 524 " --> pdb=" O   ALA A 520 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE A 529 " --> pdb=" O   TRP A 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 56
      removed outlier: 3.646A  pdb=" N   LEU B  56 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 110
      removed outlier: 3.535A  pdb=" N   ILE B 103 " --> pdb=" O   GLY B  99 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASP B 104 " --> pdb=" O   GLY B 100 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   MET B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ARG B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 126
      removed outlier: 3.604A  pdb=" N   ALA B 119 " --> pdb=" O   ASN B 115 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLU B 120 " --> pdb=" O   ALA B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
      removed outlier: 3.602A  pdb=" N   VAL B 144 " --> pdb=" O   ASN B 140 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   SER B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 184
      removed outlier: 3.990A  pdb=" N   GLN B 175 " --> pdb=" O   GLU B 171 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN B 183 " --> pdb=" O   GLY B 179 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ARG B 184 " --> pdb=" O   GLU B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 202
      removed outlier: 3.683A  pdb=" N   ALA B 200 " --> pdb=" O   ALA B 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 55
    Processing helix  chain 'C' and resid 76 through 81
    Processing helix  chain 'C' and resid 98 through 111
    Processing helix  chain 'C' and resid 114 through 126
      removed outlier: 3.772A  pdb=" N   GLU C 120 " --> pdb=" O   ALA C 116 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY C 126 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 136
      removed outlier: 3.605A  pdb=" N   TYR C 136 " --> pdb=" O   ALA C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 151
      removed outlier: 3.623A  pdb=" N   LYS C 143 " --> pdb=" O   GLY C 139 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL C 144 " --> pdb=" O   ASN C 140 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER C 145 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 184
      removed outlier: 3.564A  pdb=" N   ARG C 184 " --> pdb=" O   GLU C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 202
      removed outlier: 3.655A  pdb=" N   ALA C 200 " --> pdb=" O   ALA C 196 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 32
      removed outlier: 4.900A  pdb=" N   LEU B  15 " --> pdb=" O   GLY B  27 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ASP B  29 " --> pdb=" O   ARG B  13 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ARG B  13 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   THR B  31 " --> pdb=" O   GLU B  11 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   GLU B  11 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   LEU B  15 " --> pdb=" O   GLY B  63 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLY B  63 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 87
      removed outlier: 6.789A  pdb=" N   ALA B  85 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   ASP B 160 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL B  87 " --> pdb=" O   ASP B 160 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   LEU B 157 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   SER B 191 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LEU B 159 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   HIS B  38 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   VAL B 205 " --> pdb=" O   SER B 216 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   SER B 216 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ILE B 207 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 11
      removed outlier: 3.568A  pdb=" N   ILE C  10 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 26
      removed outlier: 4.701A  pdb=" N   LEU C  15 " --> pdb=" O   GLY C  63 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   GLY C  63 " --> pdb=" O   LEU C  15 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 39
      removed outlier: 6.482A  pdb=" N   HIS C  38 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA C  85 " --> pdb=" O   LEU C 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 205 through 208
      removed outlier: 7.089A  pdb=" N   VAL C 205 " --> pdb=" O   SER C 216 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   SER C 216 " --> pdb=" O   VAL C 205 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ILE C 207 " --> pdb=" O   VAL C 214 " (cutoff:3.500A)

    331 hydrogen bonds defined for protein.
    978 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.77

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1124
        1.30 -     1.43: 1767
        1.43 -     1.55: 4340
        1.55 -     1.68: 21
        1.68 -     1.81: 38
  Bond restraints: 7290
  Sorted by residual:
  bond pdb=" O3A ANP C 401 "
       pdb=" PB  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.554  0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" O3A ANP B 401 "
       pdb=" PB  ANP B 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.554  0.146 2.00e-02 2.50e+03 5.30e+01
  bond pdb=" CA  ALA A 275 "
       pdb=" CB  ALA A 275 "
    ideal  model  delta    sigma   weight residual
    1.530  1.449  0.082 1.48e-02 4.57e+03 3.06e+01
  bond pdb=" N3B ANP B 401 "
       pdb=" PG  ANP B 401 "
    ideal  model  delta    sigma   weight residual
    1.795  1.688  0.107 2.00e-02 2.50e+03 2.88e+01
  bond pdb=" N3B ANP C 401 "
       pdb=" PG  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.795  1.691  0.104 2.00e-02 2.50e+03 2.69e+01
  ... (remaining 7285 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.90: 9772
        3.90 -     7.80: 102
        7.80 -    11.70: 18
       11.70 -    15.59: 2
       15.59 -    19.49: 2
  Bond angle restraints: 9896
  Sorted by residual:
  angle pdb=" N   ASP A  66 "
        pdb=" CA  ASP A  66 "
        pdb=" C   ASP A  66 "
      ideal   model   delta    sigma   weight residual
     110.50   99.12   11.38 1.41e+00 5.03e-01 6.52e+01
  angle pdb=" C   GLY A 280 "
        pdb=" N   ALA A 281 "
        pdb=" CA  ALA A 281 "
      ideal   model   delta    sigma   weight residual
     122.73  109.68   13.05 1.92e+00 2.71e-01 4.62e+01
  angle pdb=" PB  ANP B 401 "
        pdb=" N3B ANP B 401 "
        pdb=" PG  ANP B 401 "
      ideal   model   delta    sigma   weight residual
     126.95  107.46   19.49 3.00e+00 1.11e-01 4.22e+01
  angle pdb=" N   ASN B 172 "
        pdb=" CA  ASN B 172 "
        pdb=" C   ASN B 172 "
      ideal   model   delta    sigma   weight residual
     113.88  106.31    7.57 1.23e+00 6.61e-01 3.79e+01
  angle pdb=" N   PRO A  65 "
        pdb=" CA  PRO A  65 "
        pdb=" C   PRO A  65 "
      ideal   model   delta    sigma   weight residual
     112.47  124.70  -12.23 2.06e+00 2.36e-01 3.52e+01
  ... (remaining 9891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.23: 4160
       32.23 -    64.46: 175
       64.46 -    96.69: 26
       96.69 -   128.92: 2
      128.92 -   161.15: 2
  Dihedral angle restraints: 4365
    sinusoidal: 1759
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CA  CYS B 202 "
           pdb=" C   CYS B 202 "
           pdb=" N   GLU B 203 "
           pdb=" CA  GLU B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.90   26.10     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" O1A ANP C 401 "
           pdb=" O3A ANP C 401 "
           pdb=" PA  ANP C 401 "
           pdb=" PB  ANP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -78.04  161.15     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" CA  GLY A 240 "
           pdb=" C   GLY A 240 "
           pdb=" N   TRP A 241 "
           pdb=" CA  TRP A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.83   22.17     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 4362 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1091
       0.096 -    0.192: 66
       0.192 -    0.288: 8
       0.288 -    0.384: 1
       0.384 -    0.480: 1
  Chirality restraints: 1167
  Sorted by residual:
  chirality pdb=" CA  ASN C  44 "
            pdb=" N   ASN C  44 "
            pdb=" C   ASN C  44 "
            pdb=" CB  ASN C  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.75e+00
  chirality pdb=" CA  ASP A  66 "
            pdb=" N   ASP A  66 "
            pdb=" C   ASP A  66 "
            pdb=" CB  ASP A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" C3' ANP B 401 "
            pdb=" C2' ANP B 401 "
            pdb=" C4' ANP B 401 "
            pdb=" O3' ANP B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 1164 not shown)

  Planarity restraints: 1225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 136 "    0.012 2.00e-02 2.50e+03   2.46e-02 6.05e+00
        pdb=" C   TYR B 136 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   TYR B 136 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER B 137 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  64 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" C   TYR A  64 "    0.037 2.00e-02 2.50e+03
        pdb=" O   TYR A  64 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PRO A  65 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  34 "   -0.011 2.00e-02 2.50e+03   2.09e-02 4.38e+00
        pdb=" C   GLU B  34 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLU B  34 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY B  35 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1222 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 34
        2.54 -     3.13: 5189
        3.13 -     3.72: 10285
        3.72 -     4.31: 14996
        4.31 -     4.90: 26269
  Nonbonded interactions: 56773
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  49 "
            pdb="MG    MG C 402 "
     model   vdw
     1.945 2.170
  nonbonded pdb=" O3G ANP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     2.034 2.170
  nonbonded pdb=" OG  SER B  49 "
            pdb="MG    MG B 402 "
     model   vdw
     2.039 2.170
  nonbonded pdb=" O3G ANP B 401 "
            pdb="MG    MG B 402 "
     model   vdw
     2.078 2.170
  nonbonded pdb=" O2B ANP C 401 "
            pdb=" O3G ANP C 401 "
     model   vdw
     2.137 3.040
  ... (remaining 56768 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 8 through 219 or resid 401 through 402))
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.910
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.510
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:13.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
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      :  0.007   0.146   7290  Z= 0.441
  Angle     :  0.998  19.492   9896  Z= 0.551
  Chirality :  0.052   0.480   1167
  Planarity :  0.005   0.040   1225
  Dihedral  : 17.978 161.154   2707
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  0.14 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.27), residues: 929
  helix: -0.47 (0.23), residues: 528
  sheet: -1.51 (0.70), residues: 58
  loop : -2.46 (0.29), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  44 
 HIS   0.007   0.001   HIS C 193 
 PHE   0.022   0.001   PHE C  40 
 TYR   0.008   0.001   TYR C  86 
 ARG   0.006   0.000   ARG A 382 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 148
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   39 VAL cc_start: 0.8529 (m) cc_final: 0.8227 (p)
REVERT: A  105 MET cc_start: 0.8016 (tpp) cc_final: 0.7703 (tpt)
REVERT: A  128 SER cc_start: 0.8006 (m) cc_final: 0.7659 (p)
REVERT: A  159 THR cc_start: 0.8254 (t) cc_final: 0.7771 (m)
REVERT: A  272 ARG cc_start: 0.6630 (mmp-170) cc_final: 0.6199 (mpt180)
REVERT: A  393 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7554 (pt0)
REVERT: B   23 ARG cc_start: 0.7078 (mtt90) cc_final: 0.6740 (mtp85)
REVERT: B  124 ARG cc_start: 0.8213 (ptp-110) cc_final: 0.7967 (ptm160)
REVERT: B  171 GLU cc_start: 0.7686 (pp20) cc_final: 0.7107 (tm-30)
REVERT: C   67 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7182 (mmp80)
REVERT: C  176 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7112 (mt0)
REVERT: C  182 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6988 (ttm170)
  outliers start: 3
  outliers final: 2
  residues processed: 151
  average time/residue: 1.5706
  time to fit residues: 247.5376
Evaluate side-chains
  99 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  493 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B  44 ASN
C 172 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.111269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.096067 restraints weight = 8413.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.43
r_work: 0.2912 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7290  Z= 0.249
  Angle     :  0.636   9.346   9896  Z= 0.314
  Chirality :  0.043   0.153   1167
  Planarity :  0.005   0.042   1225
  Dihedral  : 15.845 134.935   1226
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.00 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.28), residues: 929
  helix:  0.23 (0.23), residues: 542
  sheet: -1.07 (0.65), residues: 70
  loop : -2.31 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  44 
 HIS   0.009   0.001   HIS C 193 
 PHE   0.014   0.002   PHE C  40 
 TYR   0.010   0.002   TYR A  56 
 ARG   0.003   0.000   ARG B 124 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.8869 (p0) cc_final: 0.8665 (p0)
REVERT: A  105 MET cc_start: 0.8478 (tpp) cc_final: 0.8112 (tpt)
REVERT: A  120 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8444 (ttm-80)
REVERT: A  128 SER cc_start: 0.7931 (m) cc_final: 0.7677 (p)
REVERT: A  133 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8232 (tp)
REVERT: A  272 ARG cc_start: 0.7237 (mmp-170) cc_final: 0.7028 (tmt-80)
REVERT: A  314 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8324 (tp)
REVERT: B   23 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7198 (mtp85)
REVERT: B   26 ASP cc_start: 0.8186 (m-30) cc_final: 0.7856 (t0)
REVERT: C   67 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7654 (mmp80)
REVERT: C  176 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7387 (mt0)
REVERT: C  182 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7319 (ttm170)
REVERT: C  199 GLU cc_start: 0.8140 (pt0) cc_final: 0.7764 (pp20)
  outliers start: 15
  outliers final: 5
  residues processed: 107
  average time/residue: 1.4340
  time to fit residues: 160.9156
Evaluate side-chains
  99 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  216 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0060
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.3974

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

Flipped N/Q/H residues before XYZ refinement:
C 172 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.114481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.099127 restraints weight = 8449.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.43
r_work: 0.2956 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7290  Z= 0.154
  Angle     :  0.521   7.718   9896  Z= 0.262
  Chirality :  0.040   0.134   1167
  Planarity :  0.004   0.040   1225
  Dihedral  : 13.541 120.618   1225
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.53 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.28), residues: 929
  helix:  0.63 (0.24), residues: 545
  sheet: -0.80 (0.67), residues: 70
  loop : -2.15 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  44 
 HIS   0.005   0.001   HIS C 193 
 PHE   0.008   0.001   PHE C  40 
 TYR   0.011   0.001   TYR A 432 
 ARG   0.006   0.000   ARG A  67 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8522 (tpp) cc_final: 0.8150 (tpt)
REVERT: A  120 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8317 (ttt-90)
REVERT: A  128 SER cc_start: 0.7853 (m) cc_final: 0.7606 (p)
REVERT: A  314 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8348 (tp)
REVERT: B   23 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7174 (mtp85)
REVERT: B   26 ASP cc_start: 0.8172 (m-30) cc_final: 0.7706 (t0)
REVERT: B  171 GLU cc_start: 0.8168 (pt0) cc_final: 0.7517 (tp30)
REVERT: B  172 ASN cc_start: 0.8303 (t0) cc_final: 0.8019 (t0)
REVERT: C   67 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7688 (mmp80)
REVERT: C  176 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7393 (mt0)
REVERT: C  182 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.7275 (ttp-110)
REVERT: C  199 GLU cc_start: 0.8159 (pt0) cc_final: 0.7897 (pp20)
  outliers start: 9
  outliers final: 2
  residues processed: 100
  average time/residue: 1.5569
  time to fit residues: 162.8594
Evaluate side-chains
  95 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  169 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 88 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0970
   chunk 40 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C 172 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.111979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.096516 restraints weight = 8478.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 1.45
r_work: 0.2908 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7290  Z= 0.235
  Angle     :  0.563   7.879   9896  Z= 0.281
  Chirality :  0.042   0.136   1167
  Planarity :  0.004   0.041   1225
  Dihedral  : 13.163 119.117   1224
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.81 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.28), residues: 929
  helix:  0.77 (0.24), residues: 534
  sheet: -0.71 (0.68), residues: 70
  loop : -2.10 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  44 
 HIS   0.007   0.001   HIS C 193 
 PHE   0.010   0.001   PHE C  19 
 TYR   0.008   0.001   TYR A  56 
 ARG   0.008   0.000   ARG A  67 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.8855 (p0) cc_final: 0.8584 (p0)
REVERT: A  105 MET cc_start: 0.8537 (tpp) cc_final: 0.8163 (tpt)
REVERT: A  120 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8482 (ttm-80)
REVERT: A  128 SER cc_start: 0.7850 (m) cc_final: 0.7649 (p)
REVERT: A  314 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8406 (tp)
REVERT: A  500 MET cc_start: 0.7462 (tpp) cc_final: 0.7243 (tpt)
REVERT: B   23 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7242 (mtp85)
REVERT: B   26 ASP cc_start: 0.8148 (m-30) cc_final: 0.7901 (t0)
REVERT: B  171 GLU cc_start: 0.8138 (pt0) cc_final: 0.7746 (tp30)
REVERT: B  172 ASN cc_start: 0.8350 (t0) cc_final: 0.8099 (t0)
REVERT: C   67 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7739 (mmp80)
REVERT: C  176 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7405 (mt0)
REVERT: C  199 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7980 (pp20)
  outliers start: 10
  outliers final: 2
  residues processed: 95
  average time/residue: 1.5450
  time to fit residues: 153.3502
Evaluate side-chains
  85 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue  199 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0170
   chunk 82 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.6022

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

Flipped N/Q/H residues before XYZ refinement:
C 172 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.118465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.102786 restraints weight = 8283.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.59
r_work: 0.2917 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7290  Z= 0.181
  Angle     :  0.506   5.962   9896  Z= 0.258
  Chirality :  0.040   0.127   1167
  Planarity :  0.004   0.041   1225
  Dihedral  : 12.599 115.473   1224
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.66 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.28), residues: 929
  helix:  0.92 (0.23), residues: 541
  sheet: -0.82 (0.73), residues: 62
  loop : -1.90 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A  44 
 HIS   0.005   0.001   HIS C 193 
 PHE   0.008   0.001   PHE C  19 
 TYR   0.012   0.001   TYR A 432 
 ARG   0.008   0.000   ARG A  67 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A   93 ASP cc_start: 0.8891 (p0) cc_final: 0.8657 (p0)
REVERT: A  105 MET cc_start: 0.8560 (tpp) cc_final: 0.8170 (tpt)
REVERT: A  120 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8277 (ttt-90)
REVERT: A  128 SER cc_start: 0.7752 (m) cc_final: 0.7528 (p)
REVERT: A  314 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8330 (tp)
REVERT: A  500 MET cc_start: 0.7492 (tpp) cc_final: 0.6918 (ptt)
REVERT: B   23 ARG cc_start: 0.7774 (mtt90) cc_final: 0.7129 (mtp85)
REVERT: B  171 GLU cc_start: 0.8133 (pt0) cc_final: 0.7725 (tp30)
REVERT: B  172 ASN cc_start: 0.8283 (t0) cc_final: 0.8052 (t0)
REVERT: C   67 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7643 (mmp80)
REVERT: C  176 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7417 (mt0)
REVERT: C  199 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7958 (pp20)
REVERT: C  212 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8562 (ptpt)
  outliers start: 13
  outliers final: 4
  residues processed: 89
  average time/residue: 1.6457
  time to fit residues: 153.0087
Evaluate side-chains
  87 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue  199 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    0.0060
   chunk 81 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0970
   chunk 85 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
C 172 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.120397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.104684 restraints weight = 8233.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.60
r_work: 0.2972 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7290  Z= 0.149
  Angle     :  0.476   5.421   9896  Z= 0.245
  Chirality :  0.039   0.131   1167
  Planarity :  0.004   0.041   1225
  Dihedral  : 12.178 113.211   1224
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.50 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.28), residues: 929
  helix:  1.21 (0.23), residues: 534
  sheet: -0.76 (0.74), residues: 62
  loop : -1.83 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A  44 
 HIS   0.004   0.001   HIS C 193 
 PHE   0.006   0.001   PHE A 360 
 TYR   0.004   0.001   TYR A  56 
 ARG   0.007   0.000   ARG A  67 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A   83 GLN cc_start: 0.8285 (mm110) cc_final: 0.8071 (mm-40)
REVERT: A   93 ASP cc_start: 0.8871 (p0) cc_final: 0.8651 (p0)
REVERT: A  105 MET cc_start: 0.8564 (tpp) cc_final: 0.8184 (tpt)
REVERT: A  120 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8275 (ttt-90)
REVERT: A  314 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8329 (tp)
REVERT: A  370 MET cc_start: 0.8252 (mtt) cc_final: 0.8007 (mtt)
REVERT: A  500 MET cc_start: 0.7486 (tpp) cc_final: 0.6946 (ptt)
REVERT: B   23 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7114 (mtp85)
REVERT: B   26 ASP cc_start: 0.8138 (t0) cc_final: 0.7775 (t0)
REVERT: B  171 GLU cc_start: 0.7965 (pt0) cc_final: 0.7685 (tp30)
REVERT: B  172 ASN cc_start: 0.8271 (t0) cc_final: 0.8018 (t0)
REVERT: C   67 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7620 (mmp80)
REVERT: C  176 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7372 (mt0)
REVERT: C  199 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7832 (pp20)
  outliers start: 12
  outliers final: 4
  residues processed: 90
  average time/residue: 1.6771
  time to fit residues: 157.3874
Evaluate side-chains
  83 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue  199 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0000
   chunk 78 optimal weight:    0.0470
   chunk 30 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3682

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

Flipped N/Q/H residues before XYZ refinement:
A 385 GLN
C 172 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.102170 restraints weight = 8344.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.57
r_work: 0.2985 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7290  Z= 0.146
  Angle     :  0.469   5.132   9896  Z= 0.241
  Chirality :  0.039   0.125   1167
  Planarity :  0.004   0.040   1225
  Dihedral  : 11.898 113.143   1224
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.64 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.28), residues: 929
  helix:  1.41 (0.24), residues: 534
  sheet: -0.73 (0.73), residues: 62
  loop : -1.73 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  44 
 HIS   0.003   0.001   HIS C 193 
 PHE   0.006   0.001   PHE C  19 
 TYR   0.012   0.001   TYR A 432 
 ARG   0.008   0.000   ARG A  67 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A   83 GLN cc_start: 0.8203 (mm110) cc_final: 0.7979 (mm-40)
REVERT: A   93 ASP cc_start: 0.8826 (p0) cc_final: 0.8607 (p0)
REVERT: A  105 MET cc_start: 0.8483 (tpp) cc_final: 0.8068 (tpt)
REVERT: A  120 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8152 (ttt-90)
REVERT: A  272 ARG cc_start: 0.7822 (tmt170) cc_final: 0.7600 (tmt-80)
REVERT: A  314 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8165 (tp)
REVERT: A  370 MET cc_start: 0.8069 (mtt) cc_final: 0.7856 (mtt)
REVERT: A  500 MET cc_start: 0.7439 (tpp) cc_final: 0.6910 (ptt)
REVERT: B   23 ARG cc_start: 0.7733 (mtt90) cc_final: 0.6977 (mtp85)
REVERT: B   26 ASP cc_start: 0.8071 (t0) cc_final: 0.7687 (t0)
REVERT: B  171 GLU cc_start: 0.7872 (pt0) cc_final: 0.7589 (tp30)
REVERT: B  172 ASN cc_start: 0.8132 (t0) cc_final: 0.7875 (t0)
REVERT: C   67 ARG cc_start: 0.7962 (mmm160) cc_final: 0.7490 (mmp80)
REVERT: C  176 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7200 (mt0)
REVERT: C  199 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7676 (mm-30)
REVERT: C  203 GLU cc_start: 0.6644 (pm20) cc_final: 0.6421 (pm20)
  outliers start: 12
  outliers final: 6
  residues processed: 95
  average time/residue: 1.5999
  time to fit residues: 158.8933
Evaluate side-chains
  89 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ARG
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue  199 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 91 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 385 GLN
C  18 HIS
C 172 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.117773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.102031 restraints weight = 8353.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 1.61
r_work: 0.2950 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7290  Z= 0.212
  Angle     :  0.535   7.139   9896  Z= 0.269
  Chirality :  0.041   0.124   1167
  Planarity :  0.004   0.041   1225
  Dihedral  : 12.194 116.018   1224
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.64 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.28), residues: 929
  helix:  1.30 (0.24), residues: 528
  sheet: -0.73 (0.74), residues: 62
  loop : -1.71 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  44 
 HIS   0.006   0.001   HIS C 193 
 PHE   0.010   0.001   PHE C  19 
 TYR   0.007   0.001   TYR A  56 
 ARG   0.008   0.000   ARG A  67 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 GLN cc_start: 0.8362 (mm110) cc_final: 0.8135 (mm-40)
REVERT: A   93 ASP cc_start: 0.8865 (p0) cc_final: 0.8627 (p0)
REVERT: A  105 MET cc_start: 0.8554 (tpp) cc_final: 0.8107 (tpt)
REVERT: A  314 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8373 (tp)
REVERT: A  500 MET cc_start: 0.7594 (tpp) cc_final: 0.7065 (ptt)
REVERT: B   23 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7206 (mtp85)
REVERT: B   26 ASP cc_start: 0.8203 (t0) cc_final: 0.7992 (t0)
REVERT: C   34 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7887 (tp30)
REVERT: C   67 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7652 (mmp80)
REVERT: C  176 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7376 (mt0)
REVERT: C  199 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7967 (pp20)
  outliers start: 15
  outliers final: 8
  residues processed: 86
  average time/residue: 1.7370
  time to fit residues: 155.7966
Evaluate side-chains
  89 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ARG
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue   23 ARG
Chi-restraints excluded: chain C residue   34 GLU
Chi-restraints excluded: chain C residue  199 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
C  18 HIS
C 172 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.116809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.101046 restraints weight = 8436.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.61
r_work: 0.2943 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7290  Z= 0.238
  Angle     :  0.564   7.415   9896  Z= 0.285
  Chirality :  0.042   0.129   1167
  Planarity :  0.004   0.041   1225
  Dihedral  : 12.354 116.431   1224
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 17.07 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.28), residues: 929
  helix:  1.23 (0.23), residues: 527
  sheet: -0.71 (0.74), residues: 62
  loop : -1.73 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A  44 
 HIS   0.006   0.001   HIS C 193 
 PHE   0.010   0.001   PHE C  19 
 TYR   0.015   0.001   TYR A 432 
 ARG   0.009   0.000   ARG A  67 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 SER cc_start: 0.8474 (t) cc_final: 0.8177 (m)
REVERT: A   83 GLN cc_start: 0.8412 (mm110) cc_final: 0.8172 (mm-40)
REVERT: A   93 ASP cc_start: 0.8870 (p0) cc_final: 0.8651 (p0)
REVERT: A  105 MET cc_start: 0.8572 (tpp) cc_final: 0.8131 (tpt)
REVERT: A  314 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8405 (tp)
REVERT: A  370 MET cc_start: 0.8411 (mtt) cc_final: 0.8130 (mtt)
REVERT: A  500 MET cc_start: 0.7641 (tpp) cc_final: 0.7081 (ptt)
REVERT: B   23 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7171 (mtp85)
REVERT: B   26 ASP cc_start: 0.8242 (t0) cc_final: 0.7873 (t0)
REVERT: B   82 ARG cc_start: 0.8083 (ptp90) cc_final: 0.7763 (mtt180)
REVERT: B  172 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.7834 (m-40)
REVERT: C   23 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7151 (tmm-80)
REVERT: C   67 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7696 (mmp80)
REVERT: C  176 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7396 (mt0)
REVERT: C  199 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8037 (pp20)
  outliers start: 15
  outliers final: 6
  residues processed: 93
  average time/residue: 1.6426
  time to fit residues: 159.3488
Evaluate side-chains
  85 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  172 ASN
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue   23 ARG
Chi-restraints excluded: chain C residue  199 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0870
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0980
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
C  18 HIS
C 172 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.114504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.098403 restraints weight = 8615.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.65
r_work: 0.2965 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7290  Z= 0.171
  Angle     :  0.510   6.540   9896  Z= 0.262
  Chirality :  0.040   0.126   1167
  Planarity :  0.004   0.041   1225
  Dihedral  : 12.010 113.787   1224
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.63 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.28), residues: 929
  helix:  1.46 (0.24), residues: 523
  sheet: -0.66 (0.74), residues: 62
  loop : -1.66 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A  44 
 HIS   0.004   0.001   HIS C 193 
 PHE   0.008   0.001   PHE C  19 
 TYR   0.019   0.001   TYR A 432 
 ARG   0.008   0.000   ARG A  67 

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A   83 GLN cc_start: 0.8366 (mm110) cc_final: 0.8130 (mm-40)
REVERT: A   93 ASP cc_start: 0.8864 (p0) cc_final: 0.8653 (p0)
REVERT: A  105 MET cc_start: 0.8576 (tpp) cc_final: 0.8167 (tpt)
REVERT: A  286 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7026 (mp0)
REVERT: A  314 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8350 (tp)
REVERT: A  370 MET cc_start: 0.8304 (mtt) cc_final: 0.8013 (mtt)
REVERT: A  500 MET cc_start: 0.7590 (tpp) cc_final: 0.7001 (ptt)
REVERT: A  547 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.5746 (ptp-170)
REVERT: B   23 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7105 (mtp85)
REVERT: B   26 ASP cc_start: 0.8176 (t0) cc_final: 0.7817 (t0)
REVERT: B   82 ARG cc_start: 0.8043 (ptp90) cc_final: 0.7727 (mtt180)
REVERT: B  172 ASN cc_start: 0.8277 (t0) cc_final: 0.7754 (m-40)
REVERT: C   23 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7063 (tmm-80)
REVERT: C   34 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7875 (tp30)
REVERT: C   67 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7661 (mmp80)
REVERT: C  176 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7357 (mt0)
REVERT: C  199 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7963 (pp20)
  outliers start: 11
  outliers final: 5
  residues processed: 79
  average time/residue: 1.5791
  time to fit residues: 130.4482
Evaluate side-chains
  85 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ARG
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue   23 ARG
Chi-restraints excluded: chain C residue   34 GLU
Chi-restraints excluded: chain C residue  199 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0050
   chunk 65 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
C  18 HIS
C 172 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.118798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.103054 restraints weight = 8304.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.60
r_work: 0.2933 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7290  Z= 0.182
  Angle     :  0.517   6.345   9896  Z= 0.264
  Chirality :  0.040   0.126   1167
  Planarity :  0.004   0.041   1225
  Dihedral  : 11.978 114.405   1224
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 17.91 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.28), residues: 929
  helix:  1.50 (0.24), residues: 523
  sheet:  0.08 (0.79), residues: 52
  loop : -1.62 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A  44 
 HIS   0.005   0.001   HIS C 193 
 PHE   0.008   0.001   PHE A 365 
 TYR   0.006   0.001   TYR A  56 
 ARG   0.008   0.000   ARG A  67 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5055.97 seconds
wall clock time: 90 minutes 15.37 seconds (5415.37 seconds total)