Starting phenix.real_space_refine
on Thu Mar 13 11:35:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6k42_9912/03_2025/6k42_9912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6k42_9912/03_2025/6k42_9912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6k42_9912/03_2025/6k42_9912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6k42_9912/03_2025/6k42_9912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6k42_9912/03_2025/6k42_9912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6k42_9912/03_2025/6k42_9912.cif"
  }
  resolution = 4.1
  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=   0.000 sd=   0.010
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: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5630      2.51       5
     N    1510      2.21       5
     O    1618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8816
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1759
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2616
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 2201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2201
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 12, 'TRANS': 257}
          Chain breaks: 3
    Chain: "H"
      Number of atoms: 1801
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 233, 1793
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
      Conformer: "B"
        Number of residues, atoms: 233, 1793
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          bond proxies already assigned to first conformer: 1828
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'CZX': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LYS H 236 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS H 236 " occ=0.00
  Time building chain proxies: 6.37, per 1000 atoms: 0.72
  Number of scatterers: 8816
  At special positions: 0
  Unit cell: (112.08, 110.679, 128.892, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1618      8.00
     N    1510      7.00
     C    5630      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 217 " distance=2.03

  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: 2.26
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 13 sheets defined
      33.1% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 4.114A  pdb=" N   GLU A  14 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A  19 " --> pdb=" O   ARG A  15 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU A  23 " --> pdb=" O   ILE A  19 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.653A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.871A  pdb=" N   LYS A 248 " --> pdb=" O   HIS A 244 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 276
      removed outlier: 3.823A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.527A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASP A 309 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 351
    Processing helix  chain 'B' and resid 3 through 19
      removed outlier: 3.770A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 22
      removed outlier: 4.101A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.612A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 12 through 29
    Processing helix  chain 'R' and resid 29 through 39
    Processing helix  chain 'R' and resid 48 through 74
      removed outlier: 3.729A  pdb=" N   LEU R  64 " --> pdb=" O   LEU R  60 " (cutoff:3.500A)
      Proline residue:  R  67  - end of helix
    Processing helix  chain 'R' and resid 83 through 116
      removed outlier: 4.332A  pdb=" N   VAL R  87 " --> pdb=" O   THR R  83 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   CYS R  96 " --> pdb=" O   ASP R  92 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER R  99 " --> pdb=" O   PHE R  95 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL R 114 " --> pdb=" O   ARG R 110 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ARG R 116 " --> pdb=" O   TRP R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 117 through 122
      removed outlier: 3.942A  pdb=" N   ASN R 121 " --> pdb=" O   ALA R 117 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   SER R 122 " --> pdb=" O   LEU R 118 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 117 through 122'
    Processing helix  chain 'R' and resid 125 through 145
    Processing helix  chain 'R' and resid 169 through 181
      removed outlier: 3.858A  pdb=" N   LEU R 174 " --> pdb=" O   ALA R 170 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA R 175 " --> pdb=" O   TRP R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 202
    Processing helix  chain 'R' and resid 359 through 397
      removed outlier: 3.632A  pdb=" N   THR R 364 " --> pdb=" O   ARG R 360 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG R 365 " --> pdb=" O   ALA R 361 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS R 367 " --> pdb=" O   LEU R 363 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE R 377 " --> pdb=" O   LEU R 373 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   PHE R 380 " --> pdb=" O   VAL R 376 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL R 381 " --> pdb=" O   ILE R 377 " (cutoff:3.500A)
      Proline residue:  R 386  - end of helix
      removed outlier: 3.877A  pdb=" N   GLY R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   ALA R 395 " --> pdb=" O   TYR R 391 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 417
      removed outlier: 3.813A  pdb=" N   PHE R 410 " --> pdb=" O   GLY R 406 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 417 through 429
      Proline residue:  R 423  - end of helix
      removed outlier: 3.745A  pdb=" N   TYR R 426 " --> pdb=" O   ASN R 422 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR R 427 " --> pdb=" O   PRO R 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE R 428 " --> pdb=" O   VAL R 424 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   PHE R 429 " --> pdb=" O   ILE R 425 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 430 through 442
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190
      removed outlier: 3.800A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   HIS A 322 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 268 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.840A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62
      removed outlier: 3.527A  pdb=" N   HIS B  62 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.168A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.114A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192
      removed outlier: 4.099A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.736A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.621A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 128 through 130
      removed outlier: 3.642A  pdb=" N   ARG H 148 " --> pdb=" O   THR H 129 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 135 through 136
      removed outlier: 6.109A  pdb=" N   VAL H 135 " --> pdb=" O   GLU H 234 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   TRP H 164 " --> pdb=" O   LEU H 176 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 191 through 196

    339 hydrogen bonds defined for protein.
    966 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: 2.30

  Time building geometry restraints manager: 2.66 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: 2622
        1.34 -     1.46: 1721
        1.46 -     1.58: 4582
        1.58 -     1.70: 1
        1.70 -     1.82: 79
  Bond restraints: 9005
  Sorted by residual:
  bond pdb=" C09 CZX R 501 "
       pdb=" C12 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.385  1.529 -0.144 2.00e-02 2.50e+03 5.17e+01
  bond pdb=" C11 CZX R 501 "
       pdb=" C12 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.386  1.528 -0.142 2.00e-02 2.50e+03 5.07e+01
  bond pdb=" C08 CZX R 501 "
       pdb=" C11 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.392  1.528 -0.136 2.00e-02 2.50e+03 4.62e+01
  bond pdb=" C04 CZX R 501 "
       pdb=" C09 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.393  1.526 -0.133 2.00e-02 2.50e+03 4.41e+01
  bond pdb=" C04 CZX R 501 "
       pdb=" C05 CZX R 501 "
    ideal  model  delta    sigma   weight residual
    1.403  1.530 -0.127 2.00e-02 2.50e+03 4.01e+01
  ... (remaining 9000 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 11801
        1.94 -     3.87: 316
        3.87 -     5.81: 45
        5.81 -     7.75: 20
        7.75 -     9.69: 9
  Bond angle restraints: 12191
  Sorted by residual:
  angle pdb=" N   ILE R 396 "
        pdb=" CA  ILE R 396 "
        pdb=" C   ILE R 396 "
      ideal   model   delta    sigma   weight residual
     110.82  101.31    9.51 9.70e-01 1.06e+00 9.61e+01
  angle pdb=" C   ASN H 157 "
        pdb=" N   GLY H 158 "
        pdb=" CA  GLY H 158 "
      ideal   model   delta    sigma   weight residual
     121.70  131.39   -9.69 1.80e+00 3.09e-01 2.90e+01
  angle pdb=" C   TYR R  79 "
        pdb=" N   PHE R  80 "
        pdb=" CA  PHE R  80 "
      ideal   model   delta    sigma   weight residual
     121.54  130.87   -9.33 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" C   PHE R  80 "
        pdb=" N   ARG R  81 "
        pdb=" CA  ARG R  81 "
      ideal   model   delta    sigma   weight residual
     121.54  130.81   -9.27 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" CA  ALA R 395 "
        pdb=" C   ALA R 395 "
        pdb=" N   ILE R 396 "
      ideal   model   delta    sigma   weight residual
     118.81  113.25    5.56 1.15e+00 7.56e-01 2.34e+01
  ... (remaining 12186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.97: 5108
       14.97 -    29.95: 173
       29.95 -    44.92: 56
       44.92 -    59.89: 8
       59.89 -    74.86: 3
  Dihedral angle restraints: 5348
    sinusoidal: 2102
      harmonic: 3246
  Sorted by residual:
  dihedral pdb=" CA  PRO R 146 "
           pdb=" C   PRO R 146 "
           pdb=" N   PRO R 147 "
           pdb=" CA  PRO R 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.62   24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  ILE A  19 "
           pdb=" C   ILE A  19 "
           pdb=" N   ASP A  20 "
           pdb=" CA  ASP A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.10   33.90     1      1.00e+01 1.00e-02 1.63e+01
  ... (remaining 5345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1139
       0.061 -    0.123: 198
       0.123 -    0.184: 32
       0.184 -    0.246: 2
       0.246 -    0.307: 2
  Chirality restraints: 1373
  Sorted by residual:
  chirality pdb=" CA  ILE R 396 "
            pdb=" N   ILE R 396 "
            pdb=" C   ILE R 396 "
            pdb=" CB  ILE R 396 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" C03 CZX R 501 "
            pdb=" C04 CZX R 501 "
            pdb=" C06 CZX R 501 "
            pdb=" C07 CZX R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.76    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  CYS R 397 "
            pdb=" N   CYS R 397 "
            pdb=" C   CYS R 397 "
            pdb=" CB  CYS R 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 1370 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 146 "    0.063 5.00e-02 4.00e+02   9.39e-02 1.41e+01
        pdb=" N   PRO R 147 "   -0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO R 147 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO R 147 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 340 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   THR A 340 "    0.042 2.00e-02 2.50e+03
        pdb=" O   THR A 340 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASP A 341 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 395 "    0.011 2.00e-02 2.50e+03   2.40e-02 5.78e+00
        pdb=" C   ALA R 395 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ALA R 395 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE R 396 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2380
        2.81 -     3.33: 7240
        3.33 -     3.86: 13758
        3.86 -     4.38: 15383
        4.38 -     4.90: 27036
  Nonbonded interactions: 65797
  Sorted by model distance:
  nonbonded pdb=" OG  SER R  69 "
            pdb=" OH  TYR R  88 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   PRO R 423 "
            pdb=" OG1 THR R 427 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   LEU B  30 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" O   CYS R 397 "
            pdb=" N   CYS R 401 "
     model   vdw
     2.345 3.120
  ... (remaining 65792 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.290
  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:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.860
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
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      :  0.005   0.144   9005  Z= 0.383
  Angle     :  0.823   9.687  12191  Z= 0.478
  Chirality :  0.049   0.307   1373
  Planarity :  0.007   0.094   1537
  Dihedral  :  9.237  74.864   3241
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.78 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.37 (0.19), residues: 1095
  helix: -2.64 (0.19), residues: 340
  sheet: -2.22 (0.30), residues: 242
  loop : -3.42 (0.21), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.010   0.001   HIS R 102 
 PHE   0.031   0.002   PHE R 369 
 TYR   0.017   0.002   TYR R  79 
 ARG   0.005   0.000   ARG B  68 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 431
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.7535 (pp) cc_final: 0.7222 (pp)
REVERT: A   49 ILE cc_start: 0.6716 (pt) cc_final: 0.6462 (pt)
REVERT: A   50 VAL cc_start: 0.6760 (m) cc_final: 0.6501 (m)
REVERT: B   43 ILE cc_start: 0.7437 (mm) cc_final: 0.6307 (mm)
REVERT: B  280 LYS cc_start: 0.6658 (tptt) cc_final: 0.6209 (tptm)
REVERT: B  313 ASN cc_start: 0.7856 (t0) cc_final: 0.7340 (m-40)
REVERT: R  102 HIS cc_start: 0.6568 (m-70) cc_final: 0.5985 (m-70)
REVERT: R  414 ILE cc_start: 0.7376 (mm) cc_final: 0.7152 (mm)
REVERT: R  429 PHE cc_start: 0.6872 (m-10) cc_final: 0.6657 (m-10)
REVERT: H   58 ILE cc_start: 0.8045 (mt) cc_final: 0.7839 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 431
  average time/residue: 0.2382
  time to fit residues: 133.7032
Evaluate side-chains
  283 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 282
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 83 optimal weight:    0.1980
   chunk 46 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0070
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 52 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.3398

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 244 HIS
A 304 GLN
A 346 ASN
B  16 ASN
B  75 GLN
B 239 ASN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
B 311 HIS
R  30 ASN
R 121 ASN
** R 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 418 ASN
H 155 HIS
H 159 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.185435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.167394 restraints weight = 22794.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.170240 restraints weight = 24254.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.171185 restraints weight = 16749.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9005  Z= 0.184
  Angle     :  0.619   7.064  12191  Z= 0.332
  Chirality :  0.043   0.275   1373
  Planarity :  0.005   0.079   1537
  Dihedral  :  4.672  23.124   1225
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.20 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.22), residues: 1095
  helix: -0.63 (0.26), residues: 332
  sheet: -1.83 (0.30), residues: 249
  loop : -2.89 (0.23), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R  84 
 HIS   0.008   0.001   HIS H 155 
 PHE   0.031   0.002   PHE R 369 
 TYR   0.020   0.002   TYR H 216 
 ARG   0.007   0.001   ARG B 314 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.7128 (tpp) cc_final: 0.6877 (ttm)
REVERT: A  227 LEU cc_start: 0.7214 (mt) cc_final: 0.6835 (mt)
REVERT: A  246 SER cc_start: 0.8938 (m) cc_final: 0.8540 (m)
REVERT: B   68 ARG cc_start: 0.7782 (tpt-90) cc_final: 0.6935 (ttt-90)
REVERT: B  211 TRP cc_start: 0.7975 (m100) cc_final: 0.7763 (m100)
REVERT: B  280 LYS cc_start: 0.7038 (tptt) cc_final: 0.6563 (tptm)
REVERT: B  313 ASN cc_start: 0.7875 (t0) cc_final: 0.7493 (m-40)
REVERT: B  322 ASP cc_start: 0.6122 (t0) cc_final: 0.5904 (t0)
REVERT: R  414 ILE cc_start: 0.7596 (mm) cc_final: 0.7325 (mm)
REVERT: R  418 ASN cc_start: 0.5621 (t0) cc_final: 0.5004 (t0)
REVERT: H   93 MET cc_start: 0.5902 (tpp) cc_final: 0.5482 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1996
  time to fit residues: 90.5297
Evaluate side-chains
  257 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 257
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0270
   chunk 12 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
A 304 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
R  30 ASN
R 362 GLN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 155 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.176817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.158963 restraints weight = 20459.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.159327 restraints weight = 22640.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.160811 restraints weight = 16738.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3751 r_free = 0.3751    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3751 r_free = 0.3751    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9005  Z= 0.217
  Angle     :  0.634   7.686  12191  Z= 0.338
  Chirality :  0.043   0.240   1373
  Planarity :  0.005   0.072   1537
  Dihedral  :  4.673  22.659   1225
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.51 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.24), residues: 1095
  helix:  0.16 (0.28), residues: 338
  sheet: -1.63 (0.32), residues: 243
  loop : -2.61 (0.23), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H 111 
 HIS   0.007   0.002   HIS H 155 
 PHE   0.029   0.002   PHE R 369 
 TYR   0.015   0.002   TYR H 216 
 ARG   0.011   0.001   ARG B  49 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8260 (pt) cc_final: 0.8018 (mt)
REVERT: A  210 LYS cc_start: 0.8481 (mmtt) cc_final: 0.7931 (mmmt)
REVERT: A  227 LEU cc_start: 0.7603 (mt) cc_final: 0.7348 (mt)
REVERT: A  339 VAL cc_start: 0.8845 (t) cc_final: 0.8522 (t)
REVERT: A  346 ASN cc_start: 0.8582 (m110) cc_final: 0.8325 (m-40)
REVERT: B  251 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7317 (mmt90)
REVERT: B  261 LEU cc_start: 0.8349 (mt) cc_final: 0.8099 (mt)
REVERT: B  280 LYS cc_start: 0.6715 (tptt) cc_final: 0.6513 (tmtt)
REVERT: B  313 ASN cc_start: 0.8086 (t0) cc_final: 0.7856 (m110)
REVERT: R   25 PHE cc_start: 0.5990 (m-80) cc_final: 0.5763 (m-80)
REVERT: R  103 LEU cc_start: 0.8778 (mt) cc_final: 0.8494 (mp)
REVERT: R  414 ILE cc_start: 0.8018 (mm) cc_final: 0.7687 (mm)
REVERT: H   39 GLN cc_start: 0.6392 (tp40) cc_final: 0.5920 (tt0)
REVERT: H   58 ILE cc_start: 0.8196 (mt) cc_final: 0.7937 (mt)
REVERT: H   82 GLN cc_start: 0.6291 (pm20) cc_final: 0.5533 (mp10)
REVERT: H  103 TYR cc_start: 0.7219 (t80) cc_final: 0.6827 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 335
  average time/residue: 0.2173
  time to fit residues: 98.3355
Evaluate side-chains
  263 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0980
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0060
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
A 304 GLN
B 176 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 362 GLN
H 155 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.170692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.152101 restraints weight = 22208.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.150945 restraints weight = 23303.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.152752 restraints weight = 20666.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.5592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9005  Z= 0.214
  Angle     :  0.647   7.430  12191  Z= 0.341
  Chirality :  0.044   0.255   1373
  Planarity :  0.004   0.064   1537
  Dihedral  :  4.691  22.402   1225
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.57 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.97 (0.24), residues: 1095
  helix:  0.31 (0.27), residues: 340
  sheet: -1.42 (0.33), residues: 245
  loop : -2.41 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H 111 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.026   0.002   PHE R 369 
 TYR   0.018   0.002   TYR R 416 
 ARG   0.008   0.001   ARG H  18 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 324
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8491 (pt) cc_final: 0.8262 (mt)
REVERT: A   50 VAL cc_start: 0.6868 (m) cc_final: 0.6574 (m)
REVERT: A  210 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8107 (mmmt)
REVERT: A  227 LEU cc_start: 0.7973 (mt) cc_final: 0.7694 (mt)
REVERT: B  175 GLN cc_start: 0.8004 (pm20) cc_final: 0.7707 (pm20)
REVERT: B  251 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7651 (mtt-85)
REVERT: B  258 ASP cc_start: 0.7619 (t0) cc_final: 0.7368 (t70)
REVERT: B  280 LYS cc_start: 0.7236 (tptt) cc_final: 0.6934 (tmtt)
REVERT: B  313 ASN cc_start: 0.8291 (t0) cc_final: 0.8054 (m110)
REVERT: G   38 MET cc_start: 0.5944 (ptp) cc_final: 0.5726 (ptm)
REVERT: R   44 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7542 (mtt-85)
REVERT: R  102 HIS cc_start: 0.7489 (m-70) cc_final: 0.7278 (m-70)
REVERT: R  370 THR cc_start: 0.7264 (p) cc_final: 0.6936 (t)
REVERT: R  414 ILE cc_start: 0.7824 (mm) cc_final: 0.7539 (mm)
REVERT: R  422 ASN cc_start: 0.6851 (m-40) cc_final: 0.6589 (m110)
REVERT: H   34 MET cc_start: 0.8609 (mmt) cc_final: 0.8408 (mmt)
REVERT: H   82 GLN cc_start: 0.6471 (pm20) cc_final: 0.5649 (mp10)
REVERT: H   93 MET cc_start: 0.6289 (tpp) cc_final: 0.4946 (ttt)
REVERT: H  103 TYR cc_start: 0.7582 (t80) cc_final: 0.7309 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 325
  average time/residue: 0.2157
  time to fit residues: 94.0682
Evaluate side-chains
  272 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0050
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 346 ASN
B  16 ASN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 155 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.168232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.147978 restraints weight = 26668.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.151559 restraints weight = 31613.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.153630 restraints weight = 16195.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.6083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9005  Z= 0.211
  Angle     :  0.644   8.182  12191  Z= 0.337
  Chirality :  0.044   0.251   1373
  Planarity :  0.004   0.063   1537
  Dihedral  :  4.704  20.114   1225
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.99 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.75 (0.25), residues: 1095
  helix:  0.70 (0.28), residues: 329
  sheet: -1.36 (0.33), residues: 249
  loop : -2.34 (0.25), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.025   0.002   PHE R 369 
 TYR   0.015   0.002   TYR B  59 
 ARG   0.007   0.001   ARG B  68 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 322
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8716 (pt) cc_final: 0.8352 (mt)
REVERT: A  210 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8227 (mmmt)
REVERT: A  346 ASN cc_start: 0.8432 (m110) cc_final: 0.8211 (m-40)
REVERT: B  169 TRP cc_start: 0.8149 (m100) cc_final: 0.7926 (m100)
REVERT: B  173 THR cc_start: 0.7308 (p) cc_final: 0.7084 (p)
REVERT: B  175 GLN cc_start: 0.8097 (pm20) cc_final: 0.7639 (pm20)
REVERT: B  251 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7754 (mtt-85)
REVERT: B  258 ASP cc_start: 0.7857 (t0) cc_final: 0.7584 (t70)
REVERT: B  280 LYS cc_start: 0.7005 (tptt) cc_final: 0.6625 (tmtt)
REVERT: B  313 ASN cc_start: 0.8470 (t0) cc_final: 0.8213 (m-40)
REVERT: G   38 MET cc_start: 0.5940 (ptp) cc_final: 0.5660 (ptm)
REVERT: R   44 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7677 (mtt-85)
REVERT: R  102 HIS cc_start: 0.7546 (m-70) cc_final: 0.7326 (m-70)
REVERT: R  370 THR cc_start: 0.7267 (p) cc_final: 0.7015 (t)
REVERT: R  407 LEU cc_start: 0.6808 (mt) cc_final: 0.6560 (mt)
REVERT: R  414 ILE cc_start: 0.7773 (mm) cc_final: 0.7382 (mm)
REVERT: H   82 GLN cc_start: 0.6433 (pm20) cc_final: 0.5755 (mp10)
REVERT: H   93 MET cc_start: 0.6402 (tpp) cc_final: 0.5090 (ttt)
REVERT: H  127 VAL cc_start: 0.7246 (t) cc_final: 0.7008 (t)
REVERT: H  180 MET cc_start: 0.7197 (ttp) cc_final: 0.6960 (ttp)
REVERT: H  206 ARG cc_start: 0.7202 (mmp80) cc_final: 0.6908 (ptt180)
REVERT: H  225 LEU cc_start: 0.8561 (mp) cc_final: 0.8258 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 322
  average time/residue: 0.2217
  time to fit residues: 95.7650
Evaluate side-chains
  261 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 260
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 109 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0370
   chunk 3 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0570
   chunk 56 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  11 GLN
R  30 ASN
R 102 HIS
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 155 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.166874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.147455 restraints weight = 24233.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.149097 restraints weight = 26814.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.151068 restraints weight = 19424.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.6495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9005  Z= 0.201
  Angle     :  0.637   7.949  12191  Z= 0.335
  Chirality :  0.044   0.280   1373
  Planarity :  0.004   0.061   1537
  Dihedral  :  4.659  18.296   1225
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.05 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.68 (0.25), residues: 1095
  helix:  0.66 (0.28), residues: 335
  sheet: -1.32 (0.32), residues: 253
  loop : -2.27 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H 111 
 HIS   0.011   0.001   HIS R 102 
 PHE   0.031   0.002   PHE R  25 
 TYR   0.023   0.002   TYR R 416 
 ARG   0.006   0.000   ARG B  68 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8475 (pt) cc_final: 0.8219 (mt)
REVERT: A  210 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8181 (mmmt)
REVERT: B   86 THR cc_start: 0.8346 (p) cc_final: 0.7768 (p)
REVERT: B   88 ASN cc_start: 0.8743 (m-40) cc_final: 0.8189 (m-40)
REVERT: B  173 THR cc_start: 0.7456 (p) cc_final: 0.7226 (p)
REVERT: B  175 GLN cc_start: 0.8038 (pm20) cc_final: 0.7592 (pm20)
REVERT: B  280 LYS cc_start: 0.7062 (tptt) cc_final: 0.6753 (tmtt)
REVERT: B  322 ASP cc_start: 0.6737 (t0) cc_final: 0.6523 (t0)
REVERT: R   44 ARG cc_start: 0.8344 (mtt180) cc_final: 0.7578 (mtt-85)
REVERT: R  370 THR cc_start: 0.7202 (p) cc_final: 0.6935 (t)
REVERT: R  373 LEU cc_start: 0.8257 (mt) cc_final: 0.8026 (mt)
REVERT: R  377 ILE cc_start: 0.8417 (tp) cc_final: 0.7889 (tp)
REVERT: R  414 ILE cc_start: 0.7914 (mm) cc_final: 0.7612 (mm)
REVERT: R  427 THR cc_start: 0.8740 (p) cc_final: 0.8497 (p)
REVERT: H   82 GLN cc_start: 0.6340 (pm20) cc_final: 0.5638 (mp10)
REVERT: H   93 MET cc_start: 0.6589 (tpp) cc_final: 0.4652 (ttt)
REVERT: H   94 TYR cc_start: 0.3870 (m-10) cc_final: 0.3563 (m-10)
REVERT: H   95 TYR cc_start: 0.7179 (m-80) cc_final: 0.6681 (m-10)
REVERT: H  189 ASP cc_start: 0.7078 (t0) cc_final: 0.6867 (t0)
REVERT: H  225 LEU cc_start: 0.8491 (mp) cc_final: 0.8245 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 313
  average time/residue: 0.2141
  time to fit residues: 91.1153
Evaluate side-chains
  261 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 56 optimal weight:    0.0070
   chunk 51 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0870
   chunk 20 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 109 optimal weight:    0.4980
   chunk 76 optimal weight:    0.3980
   chunk 105 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0060
   overall best weight:    0.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 333 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 422 ASN
H  39 GLN
H 155 HIS
H 167 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.169421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.150978 restraints weight = 17305.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.152046 restraints weight = 16993.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.153232 restraints weight = 13908.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.6667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9005  Z= 0.157
  Angle     :  0.617   7.792  12191  Z= 0.323
  Chirality :  0.044   0.275   1373
  Planarity :  0.004   0.060   1537
  Dihedral  :  4.535  18.591   1225
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.05 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.53 (0.25), residues: 1095
  helix:  0.85 (0.29), residues: 332
  sheet: -1.10 (0.33), residues: 245
  loop : -2.27 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R  84 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.034   0.002   PHE R 181 
 TYR   0.019   0.001   TYR H 215 
 ARG   0.006   0.000   ARG H  98 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.8654 (pt) cc_final: 0.8441 (mt)
REVERT: A  210 LYS cc_start: 0.8453 (mmtt) cc_final: 0.7961 (mmmt)
REVERT: A  342 VAL cc_start: 0.8325 (t) cc_final: 0.7996 (p)
REVERT: A  343 ILE cc_start: 0.9216 (tp) cc_final: 0.8954 (tp)
REVERT: B   86 THR cc_start: 0.8289 (p) cc_final: 0.7770 (p)
REVERT: B   88 ASN cc_start: 0.8909 (m-40) cc_final: 0.8376 (m-40)
REVERT: B  175 GLN cc_start: 0.8073 (pm20) cc_final: 0.7675 (pm20)
REVERT: B  258 ASP cc_start: 0.7303 (t70) cc_final: 0.7052 (t0)
REVERT: B  260 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8156 (mt-10)
REVERT: B  280 LYS cc_start: 0.7038 (tptt) cc_final: 0.6781 (tmtt)
REVERT: B  322 ASP cc_start: 0.6486 (t0) cc_final: 0.6233 (t0)
REVERT: R  377 ILE cc_start: 0.8397 (tp) cc_final: 0.7948 (tp)
REVERT: R  414 ILE cc_start: 0.7862 (mm) cc_final: 0.7588 (mm)
REVERT: R  422 ASN cc_start: 0.6472 (m-40) cc_final: 0.5974 (m-40)
REVERT: H   29 PHE cc_start: 0.8829 (t80) cc_final: 0.8581 (t80)
REVERT: H   82 GLN cc_start: 0.5900 (pm20) cc_final: 0.5265 (mp10)
REVERT: H  138 THR cc_start: 0.6880 (t) cc_final: 0.6360 (m)
REVERT: H  224 PRO cc_start: 0.8105 (Cg_exo) cc_final: 0.7892 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 303
  average time/residue: 0.2101
  time to fit residues: 86.2415
Evaluate side-chains
  252 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
A 304 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 155 HIS
H 167 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.160518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.141208 restraints weight = 25944.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.143034 restraints weight = 34007.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.145114 restraints weight = 21126.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.7259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   9005  Z= 0.283
  Angle     :  0.709   7.425  12191  Z= 0.373
  Chirality :  0.046   0.266   1373
  Planarity :  0.005   0.063   1537
  Dihedral  :  4.999  19.312   1225
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.68 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.57 (0.24), residues: 1095
  helix:  0.73 (0.28), residues: 329
  sheet: -1.01 (0.33), residues: 237
  loop : -2.27 (0.24), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H 111 
 HIS   0.005   0.002   HIS B  54 
 PHE   0.033   0.002   PHE R 369 
 TYR   0.022   0.002   TYR H 223 
 ARG   0.007   0.001   ARG B  68 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7687 (mp0) cc_final: 0.7444 (mp0)
REVERT: A   19 ILE cc_start: 0.8877 (pt) cc_final: 0.8567 (mt)
REVERT: B   55 LEU cc_start: 0.8876 (mt) cc_final: 0.8675 (mt)
REVERT: B   61 MET cc_start: 0.8485 (tmm) cc_final: 0.7994 (tpp)
REVERT: B   86 THR cc_start: 0.8721 (p) cc_final: 0.7535 (t)
REVERT: B   88 ASN cc_start: 0.8742 (m-40) cc_final: 0.7973 (m-40)
REVERT: B  188 MET cc_start: 0.9027 (tpp) cc_final: 0.8651 (mpp)
REVERT: B  209 LYS cc_start: 0.7696 (mttm) cc_final: 0.7461 (mmtp)
REVERT: B  280 LYS cc_start: 0.7369 (tptt) cc_final: 0.7022 (tmtt)
REVERT: G   50 LEU cc_start: 0.7538 (tp) cc_final: 0.7285 (tp)
REVERT: R   44 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7999 (mtt180)
REVERT: R  377 ILE cc_start: 0.8621 (tp) cc_final: 0.8196 (tp)
REVERT: R  414 ILE cc_start: 0.7893 (mm) cc_final: 0.7569 (mm)
REVERT: R  422 ASN cc_start: 0.6873 (m-40) cc_final: 0.6641 (m-40)
REVERT: R  427 THR cc_start: 0.8770 (p) cc_final: 0.8562 (p)
REVERT: H   57 THR cc_start: 0.8107 (m) cc_final: 0.7765 (m)
REVERT: H   93 MET cc_start: 0.6741 (tpp) cc_final: 0.4604 (ttt)
REVERT: H   95 TYR cc_start: 0.7101 (m-10) cc_final: 0.6597 (m-10)
REVERT: H  138 THR cc_start: 0.7374 (t) cc_final: 0.6652 (m)
REVERT: H  189 ASP cc_start: 0.7304 (t0) cc_final: 0.6959 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 303
  average time/residue: 0.2245
  time to fit residues: 91.2355
Evaluate side-chains
  259 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0770
   chunk 102 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0870
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.5516

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 167 GLN
** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.161894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.143653 restraints weight = 18056.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.144156 restraints weight = 20259.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.145383 restraints weight = 15174.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.7494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9005  Z= 0.218
  Angle     :  0.683   7.315  12191  Z= 0.359
  Chirality :  0.046   0.263   1373
  Planarity :  0.004   0.061   1537
  Dihedral  :  4.886  18.870   1225
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.73 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.50 (0.25), residues: 1095
  helix:  0.82 (0.29), residues: 325
  sheet: -0.94 (0.33), residues: 241
  loop : -2.25 (0.24), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP R  84 
 HIS   0.007   0.001   HIS B 183 
 PHE   0.036   0.002   PHE R 369 
 TYR   0.028   0.002   TYR R 416 
 ARG   0.006   0.001   ARG B  68 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8681 (pt) cc_final: 0.8474 (mt)
REVERT: B   61 MET cc_start: 0.8464 (tmm) cc_final: 0.8017 (tpp)
REVERT: B   75 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7578 (mm-40)
REVERT: B   86 THR cc_start: 0.8686 (p) cc_final: 0.8075 (p)
REVERT: B   88 ASN cc_start: 0.8869 (m-40) cc_final: 0.8307 (m-40)
REVERT: B  188 MET cc_start: 0.8813 (tpp) cc_final: 0.8464 (mmm)
REVERT: B  209 LYS cc_start: 0.7701 (mttm) cc_final: 0.7423 (mmtp)
REVERT: B  280 LYS cc_start: 0.7107 (tptt) cc_final: 0.6823 (tmtt)
REVERT: G   50 LEU cc_start: 0.7496 (tp) cc_final: 0.7156 (tp)
REVERT: R   44 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7957 (mtt180)
REVERT: R  377 ILE cc_start: 0.8568 (tp) cc_final: 0.8142 (tp)
REVERT: R  414 ILE cc_start: 0.7943 (mm) cc_final: 0.7538 (mm)
REVERT: R  427 THR cc_start: 0.8658 (p) cc_final: 0.8439 (p)
REVERT: H   93 MET cc_start: 0.6594 (tpp) cc_final: 0.4235 (ttt)
REVERT: H   95 TYR cc_start: 0.7172 (m-10) cc_final: 0.6558 (m-10)
REVERT: H  138 THR cc_start: 0.7286 (t) cc_final: 0.6638 (m)
REVERT: H  149 SER cc_start: 0.6372 (p) cc_final: 0.5954 (t)
REVERT: H  189 ASP cc_start: 0.7285 (t0) cc_final: 0.7007 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.2237
  time to fit residues: 88.6389
Evaluate side-chains
  260 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 53 optimal weight:    0.0050
   chunk 41 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    0.2980
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** H 219 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.161776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.143040 restraints weight = 26017.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.146769 restraints weight = 29279.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.148392 restraints weight = 14648.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.7683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9005  Z= 0.209
  Angle     :  0.704  14.738  12191  Z= 0.363
  Chirality :  0.045   0.255   1373
  Planarity :  0.004   0.062   1537
  Dihedral  :  4.834  18.741   1225
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.42 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.53 (0.24), residues: 1095
  helix:  0.69 (0.28), residues: 340
  sheet: -0.89 (0.34), residues: 237
  loop : -2.30 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R  84 
 HIS   0.004   0.001   HIS H 155 
 PHE   0.035   0.002   PHE R 369 
 TYR   0.021   0.002   TYR B  59 
 ARG   0.006   0.001   ARG A  32 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.8409 (tmm) cc_final: 0.7941 (tpp)
REVERT: B  188 MET cc_start: 0.8841 (tpp) cc_final: 0.8487 (mmm)
REVERT: B  220 GLN cc_start: 0.7196 (mt0) cc_final: 0.6839 (mp10)
REVERT: B  280 LYS cc_start: 0.7230 (tptt) cc_final: 0.7030 (tmtt)
REVERT: B  322 ASP cc_start: 0.6116 (t0) cc_final: 0.5913 (t0)
REVERT: G   50 LEU cc_start: 0.7435 (tp) cc_final: 0.7198 (tp)
REVERT: R   44 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7939 (mtt180)
REVERT: R  171 TRP cc_start: 0.6082 (p-90) cc_final: 0.5867 (p-90)
REVERT: R  377 ILE cc_start: 0.8605 (tp) cc_final: 0.8243 (tp)
REVERT: R  414 ILE cc_start: 0.7883 (mm) cc_final: 0.7588 (mm)
REVERT: R  427 THR cc_start: 0.8629 (p) cc_final: 0.8412 (p)
REVERT: H   93 MET cc_start: 0.6637 (tpp) cc_final: 0.4447 (ttt)
REVERT: H   95 TYR cc_start: 0.7027 (m-10) cc_final: 0.6395 (m-10)
REVERT: H  138 THR cc_start: 0.7284 (t) cc_final: 0.6578 (m)
REVERT: H  149 SER cc_start: 0.6027 (p) cc_final: 0.5614 (t)
REVERT: H  189 ASP cc_start: 0.7371 (t0) cc_final: 0.7168 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 303
  average time/residue: 0.2167
  time to fit residues: 88.9250
Evaluate side-chains
  262 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    0.0670
   chunk 81 optimal weight:    0.5980
   chunk 109 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 103 optimal weight:    0.4980
   chunk 94 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
G  11 GLN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 167 GLN
** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.160861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.141420 restraints weight = 26851.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.144178 restraints weight = 32726.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.146574 restraints weight = 18285.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.7825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9005  Z= 0.215
  Angle     :  0.699  12.302  12191  Z= 0.360
  Chirality :  0.045   0.258   1373
  Planarity :  0.004   0.062   1537
  Dihedral  :  4.828  17.777   1225
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.21 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    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: -1.46 (0.25), residues: 1095
  helix:  0.70 (0.28), residues: 341
  sheet: -0.80 (0.34), residues: 237
  loop : -2.26 (0.24), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 211 
 HIS   0.011   0.001   HIS H 155 
 PHE   0.036   0.002   PHE R 369 
 TYR   0.022   0.002   TYR R 120 
 ARG   0.005   0.001   ARG B  68 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3457.97 seconds
wall clock time: 60 minutes 40.47 seconds (3640.47 seconds total)