Starting phenix.real_space_refine
on Wed Sep 17 13:20:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6k42_9912/09_2025/6k42_9912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6k42_9912/09_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_9912/09_2025/6k42_9912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2025/6k42_9912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2025/6k42_9912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2025/6k42_9912.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.54, per 1000 atoms: 0.29
  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: 0.79
  Conformation dependent library (CDL) restraints added in 390.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.30
  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: 1.27

  Time building geometry restraints manager: 1.03 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:             1.410
  Set stop_for_unknowns flag:              0.010
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.090
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.280
-------------------------------------------------------------------------------
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   9008  Z= 0.269
  Angle     :  0.823   9.687  12197  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 : 4.16
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.37 (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
 ARG   0.005   0.000   ARG B  68 
 TYR   0.017   0.002   TYR R  79 
 PHE   0.031   0.002   PHE R 369 
 TRP   0.015   0.001   TRP B 211 
 HIS   0.010   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 9005)
  covalent geometry    : angle       0.82290 (12191)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       1.11556 (    6)
  hydrogen bonds       : bond        0.16614 (  339)
  hydrogen bonds       : angle       7.06261 (  966)

*********************** 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  : 0.362 
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: 0.7228 (pp)
REVERT: A   49 ILE cc_start: 0.6716 (pt) cc_final: 0.6464 (pt)
REVERT: A   50 VAL cc_start: 0.6760 (m) cc_final: 0.6497 (m)
REVERT: B   43 ILE cc_start: 0.7437 (mm) cc_final: 0.6312 (mm)
REVERT: B  153 ASP cc_start: 0.6922 (p0) cc_final: 0.6720 (p0)
REVERT: B  280 LYS cc_start: 0.6658 (tptt) cc_final: 0.6202 (tptm)
REVERT: B  313 ASN cc_start: 0.7856 (t0) cc_final: 0.7341 (m-40)
REVERT: R  102 HIS cc_start: 0.6568 (m-70) cc_final: 0.5991 (m-70)
REVERT: R  414 ILE cc_start: 0.7376 (mm) cc_final: 0.7144 (mm)
REVERT: R  429 PHE cc_start: 0.6872 (m-10) cc_final: 0.6649 (m-10)
REVERT: H   58 ILE cc_start: 0.8045 (mt) cc_final: 0.7842 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 431
  average time/residue: 0.1143
  time to fit residues: 64.5523
Evaluate side-chains
  282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 281
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.0980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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
R 418 ASN
H 155 HIS
H 159 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.182482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.164448 restraints weight = 22871.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.164828 restraints weight = 25453.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.167156 restraints weight = 18670.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.167629 restraints weight = 11474.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.168309 restraints weight = 11285.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9008  Z= 0.146
  Angle     :  0.631   7.029  12197  Z= 0.338
  Chirality :  0.044   0.283   1373
  Planarity :  0.005   0.079   1537
  Dihedral  :  4.713  23.990   1225
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.30 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.87 (0.22), residues: 1095
  helix: -0.56 (0.26), residues: 337
  sheet: -1.74 (0.31), residues: 247
  loop : -2.96 (0.23), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 314 
 TYR   0.019   0.002   TYR H 216 
 PHE   0.032   0.002   PHE R 369 
 TRP   0.019   0.002   TRP R  84 
 HIS   0.008   0.001   HIS H 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9005)
  covalent geometry    : angle       0.63058 (12191)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       1.47090 (    6)
  hydrogen bonds       : bond        0.03823 (  339)
  hydrogen bonds       : angle       5.11849 (  966)

*********************** 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
  334 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 334
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.7098 (m) cc_final: 0.6485 (m)
REVERT: A  227 LEU cc_start: 0.7327 (mt) cc_final: 0.6999 (mt)
REVERT: A  246 SER cc_start: 0.8936 (m) cc_final: 0.8502 (m)
REVERT: A  346 ASN cc_start: 0.8895 (m-40) cc_final: 0.8640 (m-40)
REVERT: B   68 ARG cc_start: 0.7950 (tpt-90) cc_final: 0.7032 (ttt-90)
REVERT: B  280 LYS cc_start: 0.7173 (tptt) cc_final: 0.6663 (tptm)
REVERT: B  313 ASN cc_start: 0.7913 (t0) cc_final: 0.7572 (m-40)
REVERT: B  322 ASP cc_start: 0.6426 (t0) cc_final: 0.6142 (t0)
REVERT: R   65 ILE cc_start: 0.7816 (mm) cc_final: 0.7590 (tt)
REVERT: R  414 ILE cc_start: 0.7614 (mm) cc_final: 0.7379 (mm)
REVERT: R  418 ASN cc_start: 0.5633 (t0) cc_final: 0.5023 (t0)
REVERT: H   39 GLN cc_start: 0.6154 (tp40) cc_final: 0.5565 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 334
  average time/residue: 0.0903
  time to fit residues: 42.1518
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  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 97 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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
B 293 ASN
R  30 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 418 ASN
R 422 ASN
H 155 HIS
** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.171618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.151520 restraints weight = 26352.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.155520 restraints weight = 32247.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157533 restraints weight = 15511.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157569 restraints weight = 11241.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.158299 restraints weight = 10108.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3722
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3722
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.5198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9008  Z= 0.173
  Angle     :  0.671   8.095  12197  Z= 0.356
  Chirality :  0.045   0.245   1373
  Planarity :  0.005   0.072   1537
  Dihedral  :  4.875  21.339   1225
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.41 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.19 (0.24), residues: 1095
  helix:  0.18 (0.28), residues: 335
  sheet: -1.53 (0.32), residues: 242
  loop : -2.57 (0.23), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  49 
 TYR   0.016   0.002   TYR B  59 
 PHE   0.028   0.003   PHE R 369 
 TRP   0.024   0.002   TRP H 111 
 HIS   0.008   0.002   HIS H 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9005)
  covalent geometry    : angle       0.66686 (12191)
  SS BOND              : bond        0.00597 (    3)
  SS BOND              : angle       3.35870 (    6)
  hydrogen bonds       : bond        0.03857 (  339)
  hydrogen bonds       : angle       5.02772 (  966)

*********************** 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
  338 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 338
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8450 (pt) cc_final: 0.8157 (mt)
REVERT: A  210 LYS cc_start: 0.8406 (mmtt) cc_final: 0.7987 (mmmt)
REVERT: A  227 LEU cc_start: 0.7887 (mt) cc_final: 0.7537 (mt)
REVERT: A  346 ASN cc_start: 0.8672 (m-40) cc_final: 0.8444 (m-40)
REVERT: B   86 THR cc_start: 0.7679 (p) cc_final: 0.7464 (p)
REVERT: B  175 GLN cc_start: 0.8197 (pm20) cc_final: 0.7986 (pm20)
REVERT: B  251 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7839 (mmt90)
REVERT: B  280 LYS cc_start: 0.6974 (tptt) cc_final: 0.6569 (tmtt)
REVERT: B  313 ASN cc_start: 0.8261 (t0) cc_final: 0.7946 (m-40)
REVERT: G   42 GLU cc_start: 0.6425 (pp20) cc_final: 0.6208 (pp20)
REVERT: R  102 HIS cc_start: 0.7607 (m-70) cc_final: 0.7311 (m-70)
REVERT: R  362 GLN cc_start: 0.6227 (pp30) cc_final: 0.5900 (pp30)
REVERT: R  414 ILE cc_start: 0.7818 (mm) cc_final: 0.7583 (mm)
REVERT: R  422 ASN cc_start: 0.6837 (m-40) cc_final: 0.6577 (m-40)
REVERT: H   82 GLN cc_start: 0.6686 (pm20) cc_final: 0.5827 (mp10)
REVERT: H  103 TYR cc_start: 0.7737 (t80) cc_final: 0.7493 (t80)
REVERT: H  127 VAL cc_start: 0.6564 (t) cc_final: 0.6310 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 338
  average time/residue: 0.1050
  time to fit residues: 47.7542
Evaluate side-chains
  266 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   chunk 61 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
B  16 ASN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 155 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.166584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.147888 restraints weight = 19851.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.147530 restraints weight = 20922.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.148600 restraints weight = 18170.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.149586 restraints weight = 13087.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.149768 restraints weight = 12369.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.6064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9008  Z= 0.160
  Angle     :  0.653   7.284  12197  Z= 0.345
  Chirality :  0.045   0.245   1373
  Planarity :  0.004   0.062   1537
  Dihedral  :  4.856  20.824   1225
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.99 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.24), residues: 1095
  helix:  0.49 (0.28), residues: 331
  sheet: -1.55 (0.32), residues: 254
  loop : -2.45 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 242 
 TYR   0.020   0.002   TYR B  59 
 PHE   0.027   0.002   PHE R 369 
 TRP   0.024   0.002   TRP H 111 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9005)
  covalent geometry    : angle       0.65270 (12191)
  SS BOND              : bond        0.00650 (    3)
  SS BOND              : angle       1.33369 (    6)
  hydrogen bonds       : bond        0.03655 (  339)
  hydrogen bonds       : angle       4.90827 (  966)

*********************** 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
  322 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8612 (pt) cc_final: 0.8350 (mt)
REVERT: A  210 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8255 (mmmt)
REVERT: A  333 GLN cc_start: 0.8636 (tp40) cc_final: 0.8381 (tp40)
REVERT: A  346 ASN cc_start: 0.8592 (m-40) cc_final: 0.8304 (m-40)
REVERT: B   86 THR cc_start: 0.7999 (p) cc_final: 0.7752 (p)
REVERT: B  280 LYS cc_start: 0.7401 (tptt) cc_final: 0.6926 (tmtt)
REVERT: B  313 ASN cc_start: 0.8403 (t0) cc_final: 0.8101 (m-40)
REVERT: B  322 ASP cc_start: 0.6767 (t0) cc_final: 0.6513 (t0)
REVERT: R   44 ARG cc_start: 0.8417 (mtt180) cc_final: 0.7650 (mtt-85)
REVERT: R  171 TRP cc_start: 0.5613 (p-90) cc_final: 0.5395 (p-90)
REVERT: R  188 MET cc_start: 0.8110 (ttt) cc_final: 0.7901 (ttt)
REVERT: R  362 GLN cc_start: 0.5917 (pp30) cc_final: 0.5472 (pp30)
REVERT: R  414 ILE cc_start: 0.7806 (mm) cc_final: 0.7418 (mm)
REVERT: H   34 MET cc_start: 0.8357 (mmp) cc_final: 0.7804 (mmt)
REVERT: H   82 GLN cc_start: 0.6440 (pm20) cc_final: 0.5543 (mp10)
REVERT: H   93 MET cc_start: 0.6298 (tpp) cc_final: 0.4498 (ttt)
REVERT: H  103 TYR cc_start: 0.7650 (t80) cc_final: 0.7402 (t80)
REVERT: H  127 VAL cc_start: 0.7240 (t) cc_final: 0.6996 (t)
REVERT: H  225 LEU cc_start: 0.8696 (mt) cc_final: 0.8135 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.0991
  time to fit residues: 43.2545
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  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0770
   chunk 64 optimal weight:    0.9980
   chunk 100 optimal weight:    0.5980
   chunk 101 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 304 GLN
B  88 ASN
** 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 155 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.165097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.146883 restraints weight = 17465.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.147958 restraints weight = 17383.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.149030 restraints weight = 13939.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.148749 restraints weight = 10866.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.149132 restraints weight = 9717.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.6488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9008  Z= 0.138
  Angle     :  0.645   9.683  12197  Z= 0.337
  Chirality :  0.044   0.272   1373
  Planarity :  0.004   0.063   1537
  Dihedral  :  4.758  20.033   1225
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.30 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.25), residues: 1095
  helix:  0.69 (0.29), residues: 326
  sheet: -1.37 (0.32), residues: 258
  loop : -2.37 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  68 
 TYR   0.021   0.002   TYR B  59 
 PHE   0.026   0.002   PHE R 369 
 TRP   0.017   0.001   TRP R  84 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9005)
  covalent geometry    : angle       0.64376 (12191)
  SS BOND              : bond        0.00847 (    3)
  SS BOND              : angle       1.63242 (    6)
  hydrogen bonds       : bond        0.03437 (  339)
  hydrogen bonds       : angle       4.84841 (  966)

*********************** 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
  307 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 306
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8846 (pt) cc_final: 0.8490 (mt)
REVERT: A  210 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8170 (mmmt)
REVERT: A  247 MET cc_start: 0.7915 (mtp) cc_final: 0.7623 (mtm)
REVERT: A  346 ASN cc_start: 0.8642 (m-40) cc_final: 0.8314 (m-40)
REVERT: B   30 LEU cc_start: 0.6379 (mt) cc_final: 0.4875 (mt)
REVERT: B   86 THR cc_start: 0.8513 (p) cc_final: 0.8177 (p)
REVERT: B   88 ASN cc_start: 0.8813 (m110) cc_final: 0.8515 (m-40)
REVERT: B  280 LYS cc_start: 0.7312 (tptt) cc_final: 0.6844 (tmtt)
REVERT: B  322 ASP cc_start: 0.6680 (t0) cc_final: 0.6462 (t0)
REVERT: R  362 GLN cc_start: 0.5972 (pp30) cc_final: 0.5483 (pp30)
REVERT: R  377 ILE cc_start: 0.8056 (tp) cc_final: 0.7854 (tp)
REVERT: R  414 ILE cc_start: 0.7814 (mm) cc_final: 0.7477 (mm)
REVERT: R  422 ASN cc_start: 0.6419 (m-40) cc_final: 0.6180 (m-40)
REVERT: H   82 GLN cc_start: 0.6409 (pm20) cc_final: 0.5565 (mp10)
REVERT: H   93 MET cc_start: 0.6453 (tpp) cc_final: 0.4705 (ttt)
REVERT: H   95 TYR cc_start: 0.7228 (m-80) cc_final: 0.6878 (m-80)
REVERT: H  115 THR cc_start: 0.7226 (p) cc_final: 0.6972 (p)
REVERT: H  189 ASP cc_start: 0.7429 (t0) cc_final: 0.7206 (t0)
REVERT: H  206 ARG cc_start: 0.7496 (ptt90) cc_final: 0.7246 (mmp80)
REVERT: H  225 LEU cc_start: 0.8605 (mt) cc_final: 0.8151 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 307
  average time/residue: 0.0962
  time to fit residues: 40.2552
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  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0970
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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**
G  11 GLN
R  30 ASN
R 102 HIS
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 418 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 = 0.3774 r_free = 0.3774 target = 0.163228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.144444 restraints weight = 19541.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.144222 restraints weight = 21077.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.145703 restraints weight = 17131.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.146005 restraints weight = 12395.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.146438 restraints weight = 11656.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    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 = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.6911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9008  Z= 0.148
  Angle     :  0.653   7.278  12197  Z= 0.341
  Chirality :  0.045   0.238   1373
  Planarity :  0.004   0.057   1537
  Dihedral  :  4.782  18.961   1225
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.15 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.24), residues: 1095
  helix:  0.73 (0.28), residues: 330
  sheet: -1.43 (0.31), residues: 253
  loop : -2.36 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  68 
 TYR   0.022   0.002   TYR B  59 
 PHE   0.026   0.002   PHE R 369 
 TRP   0.018   0.002   TRP R  84 
 HIS   0.026   0.002   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9005)
  covalent geometry    : angle       0.65195 (12191)
  SS BOND              : bond        0.00403 (    3)
  SS BOND              : angle       1.58967 (    6)
  hydrogen bonds       : bond        0.03588 (  339)
  hydrogen bonds       : angle       4.85428 (  966)

*********************** 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
  315 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 315
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8831 (pt) cc_final: 0.8402 (mt)
REVERT: A  210 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8338 (mmmt)
REVERT: B   86 THR cc_start: 0.8686 (p) cc_final: 0.8113 (p)
REVERT: B   88 ASN cc_start: 0.8766 (m110) cc_final: 0.8500 (m-40)
REVERT: B  188 MET cc_start: 0.8854 (tpp) cc_final: 0.8456 (mpp)
REVERT: B  280 LYS cc_start: 0.7070 (tptt) cc_final: 0.6726 (tmtt)
REVERT: B  322 ASP cc_start: 0.6604 (t0) cc_final: 0.6359 (t0)
REVERT: R   44 ARG cc_start: 0.8338 (mtt180) cc_final: 0.8114 (mtt180)
REVERT: R  362 GLN cc_start: 0.5996 (pp30) cc_final: 0.5510 (pp30)
REVERT: R  414 ILE cc_start: 0.7844 (mm) cc_final: 0.7468 (mm)
REVERT: R  427 THR cc_start: 0.8782 (p) cc_final: 0.8529 (p)
REVERT: H   82 GLN cc_start: 0.6359 (pm20) cc_final: 0.5590 (mp10)
REVERT: H   93 MET cc_start: 0.6439 (tpp) cc_final: 0.4853 (ttt)
REVERT: H   95 TYR cc_start: 0.7292 (m-80) cc_final: 0.7004 (m-80)
REVERT: H  115 THR cc_start: 0.7502 (p) cc_final: 0.7173 (p)
REVERT: H  138 THR cc_start: 0.6697 (t) cc_final: 0.6229 (m)
REVERT: H  189 ASP cc_start: 0.7557 (t0) cc_final: 0.7343 (t0)
REVERT: H  224 PRO cc_start: 0.8173 (Cg_exo) cc_final: 0.7952 (Cg_endo)
REVERT: H  225 LEU cc_start: 0.8575 (mt) cc_final: 0.8054 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 315
  average time/residue: 0.0968
  time to fit residues: 41.6463
Evaluate side-chains
  269 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0870
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
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**
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 155 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.162406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.143973 restraints weight = 24449.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.147139 restraints weight = 27237.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.148346 restraints weight = 16665.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.148770 restraints weight = 11330.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.149031 restraints weight = 11316.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    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 = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.7215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9008  Z= 0.154
  Angle     :  0.666   7.277  12197  Z= 0.348
  Chirality :  0.046   0.223   1373
  Planarity :  0.004   0.063   1537
  Dihedral  :  4.913  19.512   1225
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.78 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.25), residues: 1095
  helix:  0.80 (0.28), residues: 329
  sheet: -1.39 (0.31), residues: 255
  loop : -2.36 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  18 
 TYR   0.022   0.002   TYR B  59 
 PHE   0.027   0.002   PHE R  21 
 TRP   0.022   0.002   TRP R  84 
 HIS   0.009   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9005)
  covalent geometry    : angle       0.66511 (12191)
  SS BOND              : bond        0.00519 (    3)
  SS BOND              : angle       1.43367 (    6)
  hydrogen bonds       : bond        0.03620 (  339)
  hydrogen bonds       : angle       4.84795 (  966)

*********************** 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
  314 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 314
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7585 (mp0) cc_final: 0.7372 (mp0)
REVERT: A   19 ILE cc_start: 0.8884 (pt) cc_final: 0.8610 (mt)
REVERT: A  210 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8342 (mmmt)
REVERT: B   46 ARG cc_start: 0.6894 (mtm-85) cc_final: 0.6623 (mtt90)
REVERT: B   86 THR cc_start: 0.8843 (p) cc_final: 0.7941 (t)
REVERT: B   88 ASN cc_start: 0.8820 (m110) cc_final: 0.8349 (m-40)
REVERT: B  220 GLN cc_start: 0.7124 (mt0) cc_final: 0.6611 (mp10)
REVERT: B  280 LYS cc_start: 0.7152 (tptt) cc_final: 0.6799 (tmtt)
REVERT: B  318 LEU cc_start: 0.8627 (tp) cc_final: 0.8377 (tp)
REVERT: B  322 ASP cc_start: 0.6653 (t0) cc_final: 0.6362 (t0)
REVERT: R  131 CYS cc_start: 0.8433 (m) cc_final: 0.8107 (m)
REVERT: R  362 GLN cc_start: 0.6037 (pp30) cc_final: 0.5825 (pp30)
REVERT: R  377 ILE cc_start: 0.8427 (tp) cc_final: 0.8044 (tp)
REVERT: R  414 ILE cc_start: 0.8134 (mm) cc_final: 0.7816 (mm)
REVERT: R  427 THR cc_start: 0.8734 (p) cc_final: 0.8511 (p)
REVERT: H   82 GLN cc_start: 0.6497 (pm20) cc_final: 0.5692 (mp10)
REVERT: H   93 MET cc_start: 0.6479 (tpp) cc_final: 0.4942 (ttt)
REVERT: H   95 TYR cc_start: 0.7286 (m-80) cc_final: 0.7005 (m-80)
REVERT: H  115 THR cc_start: 0.7757 (p) cc_final: 0.7410 (p)
REVERT: H  138 THR cc_start: 0.7329 (t) cc_final: 0.6811 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 314
  average time/residue: 0.0913
  time to fit residues: 39.4726
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  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  11 GLN
R  30 ASN
R 121 ASN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3728 r_free = 0.3728 target = 0.158953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.140658 restraints weight = 16829.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.140888 restraints weight = 17578.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.142348 restraints weight = 14268.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.142108 restraints weight = 10839.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.142659 restraints weight = 10054.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.7610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9008  Z= 0.181
  Angle     :  0.731  12.601  12197  Z= 0.381
  Chirality :  0.047   0.255   1373
  Planarity :  0.004   0.060   1537
  Dihedral  :  5.109  20.427   1225
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.24), residues: 1095
  helix:  0.65 (0.28), residues: 334
  sheet: -1.36 (0.31), residues: 255
  loop : -2.45 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  18 
 TYR   0.024   0.002   TYR A 302 
 PHE   0.031   0.002   PHE R  21 
 TRP   0.026   0.002   TRP R  84 
 HIS   0.004   0.001   HIS H 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 9005)
  covalent geometry    : angle       0.73078 (12191)
  SS BOND              : bond        0.00483 (    3)
  SS BOND              : angle       1.36507 (    6)
  hydrogen bonds       : bond        0.03786 (  339)
  hydrogen bonds       : angle       4.92527 (  966)

*********************** 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
  305 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7409 (mp0) cc_final: 0.7085 (mp0)
REVERT: A   19 ILE cc_start: 0.8914 (pt) cc_final: 0.8586 (mt)
REVERT: A  210 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8303 (mmmt)
REVERT: B   86 THR cc_start: 0.8927 (p) cc_final: 0.7928 (t)
REVERT: B   88 ASN cc_start: 0.8858 (m110) cc_final: 0.8373 (m-40)
REVERT: B  129 ARG cc_start: 0.6583 (ptt90) cc_final: 0.6328 (ptm160)
REVERT: B  209 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7456 (mmtp)
REVERT: B  280 LYS cc_start: 0.7177 (tptt) cc_final: 0.6767 (tmtt)
REVERT: R  131 CYS cc_start: 0.8502 (m) cc_final: 0.8175 (m)
REVERT: R  362 GLN cc_start: 0.6101 (pp30) cc_final: 0.5891 (pp30)
REVERT: R  377 ILE cc_start: 0.8570 (tp) cc_final: 0.8140 (tp)
REVERT: R  414 ILE cc_start: 0.8120 (mm) cc_final: 0.7810 (mm)
REVERT: R  422 ASN cc_start: 0.6756 (m-40) cc_final: 0.6480 (m-40)
REVERT: R  427 THR cc_start: 0.8837 (p) cc_final: 0.8621 (p)
REVERT: H   93 MET cc_start: 0.6546 (tpp) cc_final: 0.5464 (ttt)
REVERT: H  115 THR cc_start: 0.8079 (p) cc_final: 0.7729 (p)
REVERT: H  138 THR cc_start: 0.7346 (t) cc_final: 0.6898 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 305
  average time/residue: 0.1004
  time to fit residues: 41.5004
Evaluate side-chains
  267 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0770
   chunk 57 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 155 HIS
** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 220 HIS ** 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 = 0.3721 r_free = 0.3721 target = 0.158234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.139157 restraints weight = 24277.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.141291 restraints weight = 26870.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.143114 restraints weight = 18071.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.143607 restraints weight = 11399.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.143966 restraints weight = 10946.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    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 = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.7892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9008  Z= 0.159
  Angle     :  0.732  12.171  12197  Z= 0.376
  Chirality :  0.046   0.284   1373
  Planarity :  0.004   0.063   1537
  Dihedral  :  5.006  19.988   1225
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.25), residues: 1095
  helix:  0.64 (0.28), residues: 341
  sheet: -1.31 (0.31), residues: 260
  loop : -2.40 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  18 
 TYR   0.023   0.002   TYR R 416 
 PHE   0.032   0.002   PHE R  21 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.010   0.001   HIS H 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9005)
  covalent geometry    : angle       0.73167 (12191)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       1.52357 (    6)
  hydrogen bonds       : bond        0.03708 (  339)
  hydrogen bonds       : angle       4.91301 (  966)

*********************** 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
  302 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 302
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8300 (mmmt)
REVERT: A  270 LYS cc_start: 0.6799 (mmtt) cc_final: 0.6587 (mmtm)
REVERT: B   86 THR cc_start: 0.9003 (p) cc_final: 0.7922 (t)
REVERT: B   88 ASN cc_start: 0.8929 (m110) cc_final: 0.8323 (m-40)
REVERT: B  209 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7447 (mmtp)
REVERT: B  280 LYS cc_start: 0.7240 (tptt) cc_final: 0.6860 (tmtt)
REVERT: R  119 GLU cc_start: 0.7400 (pt0) cc_final: 0.7125 (pt0)
REVERT: R  131 CYS cc_start: 0.8605 (m) cc_final: 0.8251 (m)
REVERT: R  192 TYR cc_start: 0.7194 (m-80) cc_final: 0.6954 (m-10)
REVERT: R  377 ILE cc_start: 0.8627 (tp) cc_final: 0.8251 (tp)
REVERT: R  414 ILE cc_start: 0.8035 (mm) cc_final: 0.7592 (mm)
REVERT: R  422 ASN cc_start: 0.6675 (m-40) cc_final: 0.6436 (m110)
REVERT: R  427 THR cc_start: 0.8821 (p) cc_final: 0.8591 (p)
REVERT: H  138 THR cc_start: 0.7349 (t) cc_final: 0.6645 (m)
REVERT: H  218 MET cc_start: 0.8185 (ttm) cc_final: 0.7933 (ttt)
REVERT: H  224 PRO cc_start: 0.8380 (Cg_exo) cc_final: 0.8098 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 302
  average time/residue: 0.1064
  time to fit residues: 43.1137
Evaluate side-chains
  258 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0010
   chunk 75 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0060
   chunk 19 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0050
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.2416

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 331 ASN
B  88 ASN
G  11 GLN
R  30 ASN
R 168 GLN
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.161854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.143512 restraints weight = 17553.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.143825 restraints weight = 18077.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.145420 restraints weight = 14273.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.145326 restraints weight = 10304.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.145866 restraints weight = 9527.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    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 = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.7915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9008  Z= 0.126
  Angle     :  0.695  11.532  12197  Z= 0.358
  Chirality :  0.045   0.276   1373
  Planarity :  0.004   0.061   1537
  Dihedral  :  4.823  18.993   1225
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.10 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.25), residues: 1095
  helix:  0.77 (0.29), residues: 338
  sheet: -1.09 (0.32), residues: 257
  loop : -2.22 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  68 
 TYR   0.018   0.002   TYR R 416 
 PHE   0.036   0.002   PHE R  21 
 TRP   0.016   0.001   TRP R  84 
 HIS   0.014   0.001   HIS H 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9005)
  covalent geometry    : angle       0.69466 (12191)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       1.24599 (    6)
  hydrogen bonds       : bond        0.03474 (  339)
  hydrogen bonds       : angle       4.74746 (  966)

********************** 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
  307 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ILE cc_start: 0.7394 (pt) cc_final: 0.7154 (pt)
REVERT: A  210 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8123 (mmmt)
REVERT: A  229 ASP cc_start: 0.6136 (t0) cc_final: 0.5798 (t0)
REVERT: A  270 LYS cc_start: 0.6617 (mmtt) cc_final: 0.6389 (mmtm)
REVERT: B  188 MET cc_start: 0.8834 (tpp) cc_final: 0.8468 (mmm)
REVERT: B  220 GLN cc_start: 0.7309 (mt0) cc_final: 0.6943 (mp-120)
REVERT: B  280 LYS cc_start: 0.6928 (tptt) cc_final: 0.6592 (tmtt)
REVERT: R  102 HIS cc_start: 0.7889 (m170) cc_final: 0.7318 (m90)
REVERT: R  119 GLU cc_start: 0.7356 (pt0) cc_final: 0.7075 (pt0)
REVERT: R  131 CYS cc_start: 0.8552 (m) cc_final: 0.8166 (m)
REVERT: R  192 TYR cc_start: 0.7293 (m-80) cc_final: 0.7031 (m-10)
REVERT: R  377 ILE cc_start: 0.8589 (tp) cc_final: 0.8255 (tp)
REVERT: R  414 ILE cc_start: 0.7827 (mm) cc_final: 0.7328 (mm)
REVERT: R  427 THR cc_start: 0.8749 (p) cc_final: 0.8535 (p)
REVERT: H   57 THR cc_start: 0.7823 (m) cc_final: 0.7540 (m)
REVERT: H  138 THR cc_start: 0.7294 (t) cc_final: 0.6583 (m)
REVERT: H  224 PRO cc_start: 0.8357 (Cg_exo) cc_final: 0.8112 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 307
  average time/residue: 0.0971
  time to fit residues: 40.3741
Evaluate side-chains
  253 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0970
   chunk 84 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
G  11 GLN
R  30 ASN
** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 167 GLN
** H 220 HIS ** 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 = 0.3742 r_free = 0.3742 target = 0.160319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.141073 restraints weight = 26827.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.144645 restraints weight = 32593.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.146719 restraints weight = 15520.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.147095 restraints weight = 10360.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.147713 restraints weight = 10029.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    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 = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.8060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9008  Z= 0.141
  Angle     :  0.695   7.624  12197  Z= 0.362
  Chirality :  0.046   0.270   1373
  Planarity :  0.004   0.063   1537
  Dihedral  :  4.863  19.429   1225
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.92
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.25), residues: 1095
  helix:  0.64 (0.29), residues: 340
  sheet: -1.10 (0.32), residues: 248
  loop : -2.19 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  68 
 TYR   0.017   0.002   TYR R 416 
 PHE   0.029   0.002   PHE R 181 
 TRP   0.021   0.002   TRP B 211 
 HIS   0.012   0.001   HIS H 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9005)
  covalent geometry    : angle       0.69487 (12191)
  SS BOND              : bond        0.00431 (    3)
  SS BOND              : angle       1.27687 (    6)
  hydrogen bonds       : bond        0.03567 (  339)
  hydrogen bonds       : angle       4.78825 (  966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1787.47 seconds
wall clock time: 31 minutes 37.48 seconds (1897.48 seconds total)