Starting phenix.real_space_refine
on Wed Sep 17 12:26:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lrd_63326/09_2025/9lrd_63326_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lrd_63326/09_2025/9lrd_63326.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lrd_63326/09_2025/9lrd_63326.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lrd_63326/09_2025/9lrd_63326.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lrd_63326/09_2025/9lrd_63326_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lrd_63326/09_2025/9lrd_63326_neut.cif"
  }
  resolution = 3.23
  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=   0.008 sd=   0.114
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      66      5.16       5
     C    5566      2.51       5
     N    1484      2.21       5
     O    1609      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: 8725
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1757
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "C"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "E"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2186
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 8, 'TRANS': 255}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'HSM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.96, per 1000 atoms: 0.22
  Number of scatterers: 8725
  At special positions: 0
  Unit cell: (90.3778, 121.364, 122.656, 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      66     16.00
     O    1609      8.00
     N    1484      7.00
     C    5566      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 103 " - pdb=" SG  CYS B 114 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 441 " - pdb=" SG  CYS R 444 " 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: 0.74
  Conformation dependent library (CDL) restraints added in 318.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2068

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      36.5% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.608A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 3.630A  pdb=" N   ASP A 229 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 3.507A  pdb=" N   LYS A 280 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER A 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 277 through 281'
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.942A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   CYS A 286 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 282 through 286'
    Processing helix  chain 'A' and resid 296 through 311
      removed outlier: 3.811A  pdb=" N   ASP A 309 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 352
      removed outlier: 3.554A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.702A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 22
    Processing helix  chain 'C' and resid 33 through 44
      removed outlier: 3.780A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.966A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 208 through 212
      removed outlier: 3.763A  pdb=" N   VAL E 212 " --> pdb=" O   ALA E 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 55
    Processing helix  chain 'R' and resid 63 through 79
    Processing helix  chain 'R' and resid 80 through 91
    Processing helix  chain 'R' and resid 95 through 131
      removed outlier: 4.213A  pdb=" N   LEU R  99 " --> pdb=" O   LEU R  95 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 131 through 137
      removed outlier: 3.793A  pdb=" N   LYS R 137 " --> pdb=" O   LEU R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 157
    Processing helix  chain 'R' and resid 158 through 165
      removed outlier: 3.851A  pdb=" N   ILE R 162 " --> pdb=" O   TRP R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 222
    Processing helix  chain 'R' and resid 409 through 442
      removed outlier: 3.992A  pdb=" N   ALA R 413 " --> pdb=" O   ARG R 409 " (cutoff:3.500A)
      Proline residue:  R 430  - end of helix
    Processing helix  chain 'R' and resid 446 through 464
      removed outlier: 4.167A  pdb=" N   HIS R 450 " --> pdb=" O   ASN R 446 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER R 461 " --> pdb=" O   GLY R 457 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 465 through 467
      No H-bonds generated for 'chain 'R' and resid 465 through 467'
    Processing helix  chain 'R' and resid 472 through 482
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.745A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.404A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.408A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.851A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.468A  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: 6.955A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.974A  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 153
      removed outlier: 5.130A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.529A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.071A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.631A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.961A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA E  40 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   GLY E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136
      removed outlier: 6.117A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLY E 213 " --> pdb=" O   LEU E 233 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 136
      removed outlier: 6.117A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLY E 213 " --> pdb=" O   LEU E 233 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   THR E 226 " --> pdb=" O   GLN E 219 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1158 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: 1.59

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2789
        1.34 -     1.46: 2207
        1.46 -     1.58: 3823
        1.58 -     1.70: 0
        1.70 -     1.81: 95
  Bond restraints: 8914
  Sorted by residual:
  bond pdb=" N   ASP B   5 "
       pdb=" CA  ASP B   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.12e+00
  bond pdb=" N   CYS A   3 "
       pdb=" CA  CYS A   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.89e+00
  bond pdb=" N   ILE C   9 "
       pdb=" CA  ILE C   9 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.80e+00
  bond pdb=" N   VAL E   2 "
       pdb=" CA  VAL E   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.49e+00
  bond pdb=" C   VAL E  12 "
       pdb=" N   GLN E  13 "
    ideal  model  delta    sigma   weight residual
    1.331  1.352 -0.021 1.48e-02 4.57e+03 1.98e+00
  ... (remaining 8909 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 11666
        1.33 -     2.67: 336
        2.67 -     4.00: 49
        4.00 -     5.33: 6
        5.33 -     6.66: 3
  Bond angle restraints: 12060
  Sorted by residual:
  angle pdb=" N   ILE A  49 "
        pdb=" CA  ILE A  49 "
        pdb=" C   ILE A  49 "
      ideal   model   delta    sigma   weight residual
     111.58  108.14    3.44 1.06e+00 8.90e-01 1.05e+01
  angle pdb=" N   THR A 324 "
        pdb=" CA  THR A 324 "
        pdb=" C   THR A 324 "
      ideal   model   delta    sigma   weight residual
     108.34  112.25   -3.91 1.31e+00 5.83e-01 8.93e+00
  angle pdb=" C   GLU R  55 "
        pdb=" N   ARG R  56 "
        pdb=" CA  ARG R  56 "
      ideal   model   delta    sigma   weight residual
     121.54  127.09   -5.55 1.91e+00 2.74e-01 8.44e+00
  angle pdb=" N   VAL C  30 "
        pdb=" CA  VAL C  30 "
        pdb=" C   VAL C  30 "
      ideal   model   delta    sigma   weight residual
     110.42  112.97   -2.55 9.60e-01 1.09e+00 7.03e+00
  angle pdb=" N   ARG A 205 "
        pdb=" CA  ARG A 205 "
        pdb=" C   ARG A 205 "
      ideal   model   delta    sigma   weight residual
     113.55  110.43    3.12 1.26e+00 6.30e-01 6.14e+00
  ... (remaining 12055 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 4737
       17.66 -    35.32: 459
       35.32 -    52.98: 79
       52.98 -    70.64: 10
       70.64 -    88.30: 2
  Dihedral angle restraints: 5287
    sinusoidal: 2083
      harmonic: 3204
  Sorted by residual:
  dihedral pdb=" CB  CYS R 441 "
           pdb=" SG  CYS R 441 "
           pdb=" SG  CYS R 444 "
           pdb=" CB  CYS R 444 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.66   47.66     1      1.00e+01 1.00e-02 3.13e+01
  dihedral pdb=" CA  LEU A 268 "
           pdb=" C   LEU A 268 "
           pdb=" N   ASN A 269 "
           pdb=" CA  ASN A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.31  -22.69     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  SER B 245 "
           pdb=" C   SER B 245 "
           pdb=" N   ASP B 246 "
           pdb=" CA  ASP B 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.74   20.26     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 5284 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 821
       0.028 -    0.056: 364
       0.056 -    0.084: 87
       0.084 -    0.112: 54
       0.112 -    0.140: 27
  Chirality restraints: 1353
  Sorted by residual:
  chirality pdb=" CA  ILE C   9 "
            pdb=" N   ILE C   9 "
            pdb=" C   ILE C   9 "
            pdb=" CB  ILE C   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  ILE B 229 "
            pdb=" N   ILE B 229 "
            pdb=" C   ILE B 229 "
            pdb=" CB  ILE B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1350 not shown)

  Planarity restraints: 1515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 106 "   -0.032 5.00e-02 4.00e+02   4.81e-02 3.71e+00
        pdb=" N   PRO B 107 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R  41 "   -0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   THR R  41 "    0.030 2.00e-02 2.50e+03
        pdb=" O   THR R  41 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL R  42 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R  38 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.88e+00
        pdb=" C   CYS R  38 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   CYS R  38 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU R  39 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1512 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1938
        2.78 -     3.31: 8321
        3.31 -     3.84: 14251
        3.84 -     4.37: 17269
        4.37 -     4.90: 29697
  Nonbonded interactions: 71476
  Sorted by model distance:
  nonbonded pdb=" O   PHE R 199 "
            pdb=" OG1 THR R 203 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG1 THR B 143 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OE2 GLU A 245 "
            pdb=" OG  SER A 246 "
     model   vdw
     2.340 3.040
  ... (remaining 71471 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.090
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8919  Z= 0.153
  Angle     :  0.551   6.664  12070  Z= 0.329
  Chirality :  0.039   0.140   1353
  Planarity :  0.003   0.048   1515
  Dihedral  : 13.735  88.296   3204
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 10.28 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.26), residues: 1083
  helix:  0.51 (0.29), residues: 349
  sheet: -1.75 (0.29), residues: 287
  loop : -1.47 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  56 
 TYR   0.012   0.001   TYR E 178 
 PHE   0.018   0.001   PHE R 435 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8914)
  covalent geometry    : angle       0.55118 (12060)
  SS BOND              : bond        0.00161 (    5)
  SS BOND              : angle       0.63161 (   10)
  hydrogen bonds       : bond        0.19813 (  407)
  hydrogen bonds       : angle       7.65057 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 240
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8163 (t70) cc_final: 0.7386 (t-170)
REVERT: A  198 MET cc_start: 0.8617 (ttp) cc_final: 0.8415 (ttm)
REVERT: A  243 MET cc_start: 0.5701 (ttp) cc_final: 0.4679 (ppp)
REVERT: A  263 SER cc_start: 0.8937 (p) cc_final: 0.8686 (m)
REVERT: A  318 GLU cc_start: 0.6436 (tt0) cc_final: 0.6061 (tp30)
REVERT: A  333 GLN cc_start: 0.8470 (tp-100) cc_final: 0.7908 (tp40)
REVERT: B  175 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7947 (mm110)
REVERT: B  254 ASP cc_start: 0.8271 (t0) cc_final: 0.7992 (t0)
REVERT: B  268 ASN cc_start: 0.8184 (t0) cc_final: 0.7722 (t0)
REVERT: B  280 LYS cc_start: 0.8377 (tttt) cc_final: 0.8097 (tttm)
REVERT: E   83 MET cc_start: 0.7861 (mtm) cc_final: 0.7469 (mtm)
REVERT: R   53 ARG cc_start: 0.6210 (ttp80) cc_final: 0.5469 (mpt180)
REVERT: R   92 LYS cc_start: 0.8645 (pttm) cc_final: 0.8319 (ptmm)
REVERT: R  106 MET cc_start: 0.7105 (mmp) cc_final: 0.6652 (mmm)
REVERT: R  107 ASP cc_start: 0.8090 (t0) cc_final: 0.7727 (t0)
REVERT: R  109 VAL cc_start: 0.7892 (t) cc_final: 0.7615 (p)
REVERT: R  138 TYR cc_start: 0.7463 (m-80) cc_final: 0.7096 (m-80)
REVERT: R  215 LYS cc_start: 0.7337 (tttt) cc_final: 0.7028 (mtmm)
REVERT: R  452 PHE cc_start: 0.7542 (t80) cc_final: 0.7293 (t80)
REVERT: R  466 LEU cc_start: 0.8415 (mt) cc_final: 0.8205 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 241
  average time/residue: 0.1266
  time to fit residues: 39.2466
Evaluate side-chains
  156 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  444 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 213 HIS
B  88 ASN
B 110 ASN
B 183 HIS
B 266 HIS
B 293 ASN
B 340 ASN
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN
E 220 HIS
R  59 HIS
R 416 GLN
R 460 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.189108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.141594 restraints weight = 11338.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.74
r_work: 0.3480 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8919  Z= 0.150
  Angle     :  0.641   8.924  12070  Z= 0.338
  Chirality :  0.044   0.217   1353
  Planarity :  0.004   0.047   1515
  Dihedral  :  4.954  58.553   1199
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 13.96 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.25), residues: 1083
  helix:  1.22 (0.28), residues: 358
  sheet: -1.46 (0.29), residues: 283
  loop : -1.36 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 214 
 TYR   0.012   0.002   TYR R  87 
 PHE   0.026   0.002   PHE A 250 
 TRP   0.012   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8914)
  covalent geometry    : angle       0.63530 (12060)
  SS BOND              : bond        0.00743 (    5)
  SS BOND              : angle       3.05900 (   10)
  hydrogen bonds       : bond        0.04647 (  407)
  hydrogen bonds       : angle       5.20367 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8189 (t70) cc_final: 0.7673 (t70)
REVERT: A  243 MET cc_start: 0.5402 (ttp) cc_final: 0.4357 (ppp)
REVERT: A  247 MET cc_start: 0.5120 (OUTLIER) cc_final: 0.4852 (pmm)
REVERT: A  318 GLU cc_start: 0.6381 (tt0) cc_final: 0.6117 (tp30)
REVERT: A  333 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8031 (tp40)
REVERT: B  197 ARG cc_start: 0.8036 (ptm160) cc_final: 0.7741 (ptm160)
REVERT: B  268 ASN cc_start: 0.8287 (t0) cc_final: 0.7909 (t0)
REVERT: B  280 LYS cc_start: 0.8364 (tttt) cc_final: 0.8055 (tttm)
REVERT: E   65 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7763 (tptt)
REVERT: E   83 MET cc_start: 0.7994 (mtm) cc_final: 0.7769 (mtm)
REVERT: E  216 TYR cc_start: 0.7714 (m-80) cc_final: 0.7454 (m-80)
REVERT: R   53 ARG cc_start: 0.6401 (ttp80) cc_final: 0.5973 (tpp-160)
REVERT: R   90 MET cc_start: 0.6498 (mmm) cc_final: 0.6287 (mmm)
REVERT: R   92 LYS cc_start: 0.8817 (pttm) cc_final: 0.8506 (ptmm)
REVERT: R  106 MET cc_start: 0.7045 (mmp) cc_final: 0.6660 (mmm)
REVERT: R  109 VAL cc_start: 0.8008 (t) cc_final: 0.7785 (p)
REVERT: R  138 TYR cc_start: 0.7519 (m-80) cc_final: 0.7241 (m-10)
REVERT: R  181 GLU cc_start: 0.8270 (tp30) cc_final: 0.7829 (tt0)
REVERT: R  215 LYS cc_start: 0.7936 (tttt) cc_final: 0.7422 (mtmm)
  outliers start: 28
  outliers final: 14
  residues processed: 213
  average time/residue: 0.1179
  time to fit residues: 32.7508
Evaluate side-chains
  182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  444 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    0.4980
   chunk 57 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 71 optimal weight:    9.9990
   chunk 55 optimal weight:   30.0000
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN
R  84 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.188896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.142202 restraints weight = 11190.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 2.69
r_work: 0.3533 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8919  Z= 0.135
  Angle     :  0.603  10.150  12070  Z= 0.313
  Chirality :  0.043   0.142   1353
  Planarity :  0.004   0.044   1515
  Dihedral  :  4.842  53.060   1199
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.94 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.26), residues: 1083
  helix:  1.25 (0.27), residues: 370
  sheet: -1.15 (0.31), residues: 272
  loop : -1.30 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 214 
 TYR   0.023   0.001   TYR R 185 
 PHE   0.026   0.002   PHE A 250 
 TRP   0.011   0.001   TRP R 455 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8914)
  covalent geometry    : angle       0.60201 (12060)
  SS BOND              : bond        0.00477 (    5)
  SS BOND              : angle       1.31418 (   10)
  hydrogen bonds       : bond        0.04114 (  407)
  hydrogen bonds       : angle       4.89237 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 177
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8117 (t70) cc_final: 0.7700 (t-170)
REVERT: A  243 MET cc_start: 0.5472 (ttp) cc_final: 0.4491 (ppp)
REVERT: A  247 MET cc_start: 0.5080 (OUTLIER) cc_final: 0.4862 (pmm)
REVERT: A  273 LEU cc_start: 0.7402 (tt) cc_final: 0.7059 (tt)
REVERT: A  318 GLU cc_start: 0.6516 (tt0) cc_final: 0.6205 (tp30)
REVERT: A  333 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8060 (tp40)
REVERT: B  161 SER cc_start: 0.8331 (t) cc_final: 0.8042 (p)
REVERT: B  197 ARG cc_start: 0.7910 (ptm160) cc_final: 0.7670 (ptm160)
REVERT: B  217 MET cc_start: 0.7434 (ptt) cc_final: 0.7204 (ptt)
REVERT: B  268 ASN cc_start: 0.8269 (t0) cc_final: 0.7869 (t0)
REVERT: B  269 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7087 (mm)
REVERT: B  280 LYS cc_start: 0.8323 (tttt) cc_final: 0.8054 (tttm)
REVERT: E   65 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7666 (tppt)
REVERT: E   83 MET cc_start: 0.7901 (mtm) cc_final: 0.7688 (mtm)
REVERT: E  183 LEU cc_start: 0.7783 (mt) cc_final: 0.7519 (mp)
REVERT: R   53 ARG cc_start: 0.6339 (ttp80) cc_final: 0.5939 (tpp-160)
REVERT: R   92 LYS cc_start: 0.8842 (pttm) cc_final: 0.8460 (ptmm)
REVERT: R   93 TRP cc_start: 0.7140 (t-100) cc_final: 0.6925 (t-100)
REVERT: R  106 MET cc_start: 0.7036 (mmp) cc_final: 0.6663 (mmm)
REVERT: R  109 VAL cc_start: 0.8139 (t) cc_final: 0.7889 (p)
REVERT: R  138 TYR cc_start: 0.7465 (m-80) cc_final: 0.7163 (m-10)
REVERT: R  215 LYS cc_start: 0.7929 (tttt) cc_final: 0.7403 (mtmm)
  outliers start: 27
  outliers final: 17
  residues processed: 197
  average time/residue: 0.1147
  time to fit residues: 29.7870
Evaluate side-chains
  173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue  180 CYS
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  444 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN
R  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.185884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.138194 restraints weight = 11384.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.71
r_work: 0.3426 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8919  Z= 0.208
  Angle     :  0.653   9.040  12070  Z= 0.343
  Chirality :  0.045   0.142   1353
  Planarity :  0.004   0.037   1515
  Dihedral  :  5.076  43.158   1199
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.63 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.26), residues: 1083
  helix:  1.04 (0.27), residues: 370
  sheet: -1.17 (0.30), residues: 278
  loop : -1.25 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 214 
 TYR   0.027   0.002   TYR R 185 
 PHE   0.021   0.002   PHE A 250 
 TRP   0.011   0.002   TRP E  36 
 HIS   0.006   0.002   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 8914)
  covalent geometry    : angle       0.65275 (12060)
  SS BOND              : bond        0.01481 (    5)
  SS BOND              : angle       1.03932 (   10)
  hydrogen bonds       : bond        0.04586 (  407)
  hydrogen bonds       : angle       4.90483 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 163
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8033 (t70) cc_final: 0.7224 (t-90)
REVERT: A  243 MET cc_start: 0.5392 (ttp) cc_final: 0.4483 (ppp)
REVERT: A  247 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4988 (pmm)
REVERT: A  266 LEU cc_start: 0.6721 (tp) cc_final: 0.6413 (mp)
REVERT: A  318 GLU cc_start: 0.6576 (tt0) cc_final: 0.6322 (tp30)
REVERT: A  333 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7996 (tp40)
REVERT: B  197 ARG cc_start: 0.8079 (ptm160) cc_final: 0.7822 (ptm160)
REVERT: B  268 ASN cc_start: 0.8376 (t0) cc_final: 0.8004 (t0)
REVERT: B  280 LYS cc_start: 0.8355 (tttt) cc_final: 0.8134 (tttm)
REVERT: E   65 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7893 (tptt)
REVERT: E   83 MET cc_start: 0.7919 (mtm) cc_final: 0.7620 (mtm)
REVERT: E  183 LEU cc_start: 0.7777 (mt) cc_final: 0.7496 (mp)
REVERT: R   53 ARG cc_start: 0.6430 (ttp80) cc_final: 0.6014 (tpp-160)
REVERT: R   92 LYS cc_start: 0.8910 (pttm) cc_final: 0.8496 (ptmm)
REVERT: R  106 MET cc_start: 0.7060 (mmp) cc_final: 0.6774 (mmm)
REVERT: R  123 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8211 (mt)
REVERT: R  138 TYR cc_start: 0.7536 (m-80) cc_final: 0.7193 (m-10)
REVERT: R  215 LYS cc_start: 0.7916 (tttt) cc_final: 0.7431 (mtmm)
  outliers start: 38
  outliers final: 26
  residues processed: 189
  average time/residue: 0.1116
  time to fit residues: 27.5039
Evaluate side-chains
  185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue   76 VAL
Chi-restraints excluded: chain R residue  122 CYS
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  180 CYS
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  444 CYS
Chi-restraints excluded: chain R residue  470 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 21 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.188011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.140470 restraints weight = 11278.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.73
r_work: 0.3441 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8919  Z= 0.141
  Angle     :  0.611   9.437  12070  Z= 0.318
  Chirality :  0.043   0.139   1353
  Planarity :  0.004   0.054   1515
  Dihedral  :  4.806  36.781   1199
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.73 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.26), residues: 1083
  helix:  1.23 (0.27), residues: 370
  sheet: -0.99 (0.31), residues: 274
  loop : -1.19 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 214 
 TYR   0.025   0.001   TYR R 185 
 PHE   0.020   0.002   PHE B 253 
 TRP   0.010   0.001   TRP R 455 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8914)
  covalent geometry    : angle       0.61013 (12060)
  SS BOND              : bond        0.00706 (    5)
  SS BOND              : angle       1.29867 (   10)
  hydrogen bonds       : bond        0.03947 (  407)
  hydrogen bonds       : angle       4.72235 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8170 (t70) cc_final: 0.7239 (t-90)
REVERT: A  263 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8554 (p)
REVERT: A  266 LEU cc_start: 0.6789 (tp) cc_final: 0.6490 (mp)
REVERT: A  296 TYR cc_start: 0.6101 (p90) cc_final: 0.4834 (p90)
REVERT: A  318 GLU cc_start: 0.6348 (tt0) cc_final: 0.6148 (tp30)
REVERT: A  333 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7926 (tp40)
REVERT: B  268 ASN cc_start: 0.8358 (t0) cc_final: 0.7982 (t0)
REVERT: B  280 LYS cc_start: 0.8298 (tttt) cc_final: 0.8077 (tttm)
REVERT: C   21 MET cc_start: 0.8941 (mmm) cc_final: 0.8661 (tpp)
REVERT: E   65 LYS cc_start: 0.8122 (ttmm) cc_final: 0.7642 (tppt)
REVERT: E   83 MET cc_start: 0.7996 (mtm) cc_final: 0.7786 (mtm)
REVERT: E  174 GLN cc_start: 0.7958 (tt0) cc_final: 0.7682 (mm-40)
REVERT: E  183 LEU cc_start: 0.7700 (mt) cc_final: 0.7399 (mp)
REVERT: R   46 LEU cc_start: 0.7694 (mt) cc_final: 0.7216 (pp)
REVERT: R   53 ARG cc_start: 0.6460 (ttp80) cc_final: 0.5750 (mpt180)
REVERT: R   92 LYS cc_start: 0.8754 (pttm) cc_final: 0.8401 (ptmm)
REVERT: R   93 TRP cc_start: 0.7190 (t-100) cc_final: 0.6909 (t-100)
REVERT: R  106 MET cc_start: 0.6974 (mmp) cc_final: 0.6503 (mmp)
REVERT: R  138 TYR cc_start: 0.7547 (m-80) cc_final: 0.7187 (m-10)
REVERT: R  215 LYS cc_start: 0.7890 (tttt) cc_final: 0.7412 (mtmm)
  outliers start: 30
  outliers final: 24
  residues processed: 194
  average time/residue: 0.1111
  time to fit residues: 28.4519
Evaluate side-chains
  188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  147 CYS
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  180 CYS
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  444 CYS
Chi-restraints excluded: chain R residue  476 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0980
   chunk 55 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.189860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.144241 restraints weight = 11252.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.60
r_work: 0.3560 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8919  Z= 0.133
  Angle     :  0.633  10.433  12070  Z= 0.324
  Chirality :  0.043   0.269   1353
  Planarity :  0.004   0.058   1515
  Dihedral  :  4.609  26.765   1199
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.73 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.26), residues: 1083
  helix:  1.38 (0.27), residues: 371
  sheet: -0.93 (0.31), residues: 270
  loop : -1.07 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 214 
 TYR   0.027   0.001   TYR A 296 
 PHE   0.021   0.002   PHE E 200 
 TRP   0.010   0.001   TRP R 455 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8914)
  covalent geometry    : angle       0.62977 (12060)
  SS BOND              : bond        0.00626 (    5)
  SS BOND              : angle       2.42556 (   10)
  hydrogen bonds       : bond        0.03761 (  407)
  hydrogen bonds       : angle       4.62995 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8162 (t70) cc_final: 0.7143 (t-90)
REVERT: A  243 MET cc_start: 0.5334 (ppp) cc_final: 0.4823 (ppp)
REVERT: A  263 SER cc_start: 0.8799 (m) cc_final: 0.8572 (p)
REVERT: A  266 LEU cc_start: 0.6706 (tp) cc_final: 0.6460 (mp)
REVERT: A  318 GLU cc_start: 0.6344 (tt0) cc_final: 0.6121 (tp30)
REVERT: A  333 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7897 (tp40)
REVERT: B  268 ASN cc_start: 0.8299 (t0) cc_final: 0.7950 (t0)
REVERT: B  280 LYS cc_start: 0.8210 (tttt) cc_final: 0.8009 (tttm)
REVERT: C   21 MET cc_start: 0.8881 (mmm) cc_final: 0.8605 (tpp)
REVERT: C   37 LEU cc_start: 0.6145 (mt) cc_final: 0.5501 (mt)
REVERT: E   65 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7560 (tppt)
REVERT: E  174 GLN cc_start: 0.7889 (tt0) cc_final: 0.7530 (mm-40)
REVERT: E  183 LEU cc_start: 0.7717 (mt) cc_final: 0.7429 (mp)
REVERT: R   46 LEU cc_start: 0.7619 (mt) cc_final: 0.7064 (pp)
REVERT: R   53 ARG cc_start: 0.5982 (ttp80) cc_final: 0.5284 (mpt180)
REVERT: R   93 TRP cc_start: 0.7165 (t-100) cc_final: 0.6798 (t-100)
REVERT: R  106 MET cc_start: 0.7012 (mmp) cc_final: 0.6559 (mmp)
REVERT: R  138 TYR cc_start: 0.7527 (m-80) cc_final: 0.7174 (m-10)
REVERT: R  215 LYS cc_start: 0.7868 (tttt) cc_final: 0.7348 (mtmm)
  outliers start: 32
  outliers final: 24
  residues processed: 193
  average time/residue: 0.1106
  time to fit residues: 28.3243
Evaluate side-chains
  189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  147 CYS
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue   76 VAL
Chi-restraints excluded: chain R residue  122 CYS
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  180 CYS
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  221 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 100 optimal weight:    0.0070
   chunk 95 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 99 optimal weight:    0.6980
   chunk 55 optimal weight:   20.0000
   chunk 85 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.190850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.145916 restraints weight = 11183.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.96
r_work: 0.3574 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8919  Z= 0.121
  Angle     :  0.638  11.347  12070  Z= 0.323
  Chirality :  0.042   0.171   1353
  Planarity :  0.003   0.033   1515
  Dihedral  :  4.534  26.674   1198
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.09 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.26), residues: 1083
  helix:  1.72 (0.28), residues: 365
  sheet: -0.77 (0.33), residues: 253
  loop : -1.02 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 206 
 TYR   0.021   0.001   TYR R 185 
 PHE   0.020   0.001   PHE B 151 
 TRP   0.011   0.001   TRP R 165 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8914)
  covalent geometry    : angle       0.63190 (12060)
  SS BOND              : bond        0.00524 (    5)
  SS BOND              : angle       3.02128 (   10)
  hydrogen bonds       : bond        0.03552 (  407)
  hydrogen bonds       : angle       4.59314 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8117 (t70) cc_final: 0.7304 (t70)
REVERT: A  296 TYR cc_start: 0.6712 (p90) cc_final: 0.6492 (p90)
REVERT: A  318 GLU cc_start: 0.6366 (tt0) cc_final: 0.6147 (tp30)
REVERT: A  333 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7875 (tp40)
REVERT: B   76 ASP cc_start: 0.7332 (t0) cc_final: 0.7032 (t70)
REVERT: B  101 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8270 (mtp)
REVERT: B  268 ASN cc_start: 0.8263 (t0) cc_final: 0.7922 (t0)
REVERT: C   21 MET cc_start: 0.8797 (mmm) cc_final: 0.8378 (tpp)
REVERT: C   37 LEU cc_start: 0.5962 (mt) cc_final: 0.5089 (mt)
REVERT: E   65 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7374 (tppt)
REVERT: E  174 GLN cc_start: 0.7863 (tt0) cc_final: 0.7439 (mm-40)
REVERT: E  183 LEU cc_start: 0.7700 (mt) cc_final: 0.7399 (mp)
REVERT: R   46 LEU cc_start: 0.7580 (mt) cc_final: 0.7053 (pp)
REVERT: R   53 ARG cc_start: 0.5923 (ttp80) cc_final: 0.5219 (mpt180)
REVERT: R   93 TRP cc_start: 0.6994 (t-100) cc_final: 0.6703 (t-100)
REVERT: R  106 MET cc_start: 0.7001 (mmp) cc_final: 0.6580 (mmp)
REVERT: R  107 ASP cc_start: 0.8276 (t0) cc_final: 0.7907 (t0)
REVERT: R  138 TYR cc_start: 0.7524 (m-80) cc_final: 0.7167 (m-10)
REVERT: R  215 LYS cc_start: 0.7890 (tttt) cc_final: 0.7351 (mtmm)
  outliers start: 27
  outliers final: 22
  residues processed: 194
  average time/residue: 0.1150
  time to fit residues: 29.3208
Evaluate side-chains
  185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  147 CYS
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  155 SER
Chi-restraints excluded: chain R residue  180 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0770
   chunk 4 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   overall best weight:    0.7142

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
E  35 HIS
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.190760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.145561 restraints weight = 11116.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 3.02
r_work: 0.3562 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.4296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8919  Z= 0.134
  Angle     :  0.660  12.791  12070  Z= 0.332
  Chirality :  0.042   0.154   1353
  Planarity :  0.004   0.033   1515
  Dihedral  :  4.533  29.463   1198
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 20.57 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.27), residues: 1083
  helix:  1.76 (0.28), residues: 366
  sheet: -0.72 (0.33), residues: 253
  loop : -0.97 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 242 
 TYR   0.020   0.001   TYR R 185 
 PHE   0.020   0.002   PHE A 250 
 TRP   0.011   0.001   TRP R 165 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8914)
  covalent geometry    : angle       0.65549 (12060)
  SS BOND              : bond        0.00614 (    5)
  SS BOND              : angle       2.66752 (   10)
  hydrogen bonds       : bond        0.03578 (  407)
  hydrogen bonds       : angle       4.58475 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8138 (t70) cc_final: 0.7405 (t70)
REVERT: A  266 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6095 (mp)
REVERT: A  318 GLU cc_start: 0.6321 (tt0) cc_final: 0.6048 (tp30)
REVERT: A  333 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7862 (tp40)
REVERT: B   76 ASP cc_start: 0.7299 (t0) cc_final: 0.6920 (t70)
REVERT: B  164 THR cc_start: 0.6880 (p) cc_final: 0.6581 (p)
REVERT: B  268 ASN cc_start: 0.8197 (t0) cc_final: 0.7909 (t0)
REVERT: C   21 MET cc_start: 0.8771 (mmm) cc_final: 0.8432 (tpp)
REVERT: E   65 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7328 (tppt)
REVERT: E  174 GLN cc_start: 0.7864 (tt0) cc_final: 0.7451 (mm-40)
REVERT: E  183 LEU cc_start: 0.7694 (mt) cc_final: 0.7388 (mp)
REVERT: R   46 LEU cc_start: 0.7576 (mt) cc_final: 0.7031 (pp)
REVERT: R   53 ARG cc_start: 0.5973 (ttp80) cc_final: 0.5264 (mpt180)
REVERT: R   93 TRP cc_start: 0.6952 (t-100) cc_final: 0.6728 (t-100)
REVERT: R  106 MET cc_start: 0.7029 (mmp) cc_final: 0.6622 (mmp)
REVERT: R  138 TYR cc_start: 0.7583 (m-80) cc_final: 0.7226 (m-10)
REVERT: R  215 LYS cc_start: 0.7903 (tttt) cc_final: 0.7378 (mtmm)
  outliers start: 28
  outliers final: 24
  residues processed: 188
  average time/residue: 0.1229
  time to fit residues: 30.5101
Evaluate side-chains
  186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  147 CYS
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   76 VAL
Chi-restraints excluded: chain R residue  122 CYS
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  155 SER
Chi-restraints excluded: chain R residue  180 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 91 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.190789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.145550 restraints weight = 11148.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.99
r_work: 0.3544 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.4432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8919  Z= 0.145
  Angle     :  0.669  10.202  12070  Z= 0.338
  Chirality :  0.043   0.167   1353
  Planarity :  0.004   0.053   1515
  Dihedral  :  4.586  29.909   1198
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 21.72 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.27), residues: 1083
  helix:  1.77 (0.28), residues: 366
  sheet: -0.59 (0.34), residues: 248
  loop : -0.99 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 242 
 TYR   0.024   0.001   TYR A 296 
 PHE   0.021   0.002   PHE A 250 
 TRP   0.013   0.001   TRP R 165 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8914)
  covalent geometry    : angle       0.66589 (12060)
  SS BOND              : bond        0.00540 (    5)
  SS BOND              : angle       2.37234 (   10)
  hydrogen bonds       : bond        0.03661 (  407)
  hydrogen bonds       : angle       4.56341 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8171 (t70) cc_final: 0.7445 (t70)
REVERT: A  243 MET cc_start: 0.5064 (ppp) cc_final: 0.4698 (ppp)
REVERT: A  266 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6264 (mp)
REVERT: A  318 GLU cc_start: 0.6317 (tt0) cc_final: 0.6068 (tp30)
REVERT: A  333 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7764 (tp40)
REVERT: B   76 ASP cc_start: 0.7386 (t0) cc_final: 0.6977 (t70)
REVERT: B  164 THR cc_start: 0.6837 (p) cc_final: 0.6537 (p)
REVERT: C   21 MET cc_start: 0.8805 (mmm) cc_final: 0.8459 (tpp)
REVERT: E   65 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7378 (tppt)
REVERT: E  174 GLN cc_start: 0.7862 (tt0) cc_final: 0.7465 (mm-40)
REVERT: E  183 LEU cc_start: 0.7658 (mt) cc_final: 0.7343 (mp)
REVERT: R   46 LEU cc_start: 0.7584 (mt) cc_final: 0.7037 (pp)
REVERT: R   53 ARG cc_start: 0.5986 (ttp80) cc_final: 0.5267 (mpt180)
REVERT: R  106 MET cc_start: 0.7048 (mmp) cc_final: 0.6817 (mmm)
REVERT: R  138 TYR cc_start: 0.7649 (m-80) cc_final: 0.7266 (m-10)
REVERT: R  193 MET cc_start: 0.6129 (tpp) cc_final: 0.5622 (tpt)
REVERT: R  215 LYS cc_start: 0.7882 (tttt) cc_final: 0.7388 (mtmm)
  outliers start: 29
  outliers final: 26
  residues processed: 189
  average time/residue: 0.1211
  time to fit residues: 30.2119
Evaluate side-chains
  186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  147 CYS
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   76 VAL
Chi-restraints excluded: chain R residue  122 CYS
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  155 SER
Chi-restraints excluded: chain R residue  180 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 4 optimal weight:    0.0470
   chunk 92 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.190997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.145708 restraints weight = 11096.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.82
r_work: 0.3557 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.4588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8919  Z= 0.133
  Angle     :  0.684  12.198  12070  Z= 0.342
  Chirality :  0.043   0.192   1353
  Planarity :  0.004   0.047   1515
  Dihedral  :  4.694  30.612   1198
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.41 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.27), residues: 1083
  helix:  1.84 (0.28), residues: 366
  sheet: -0.72 (0.34), residues: 255
  loop : -0.94 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 242 
 TYR   0.019   0.001   TYR R 185 
 PHE   0.020   0.002   PHE A 250 
 TRP   0.014   0.001   TRP R 165 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8914)
  covalent geometry    : angle       0.68016 (12060)
  SS BOND              : bond        0.00554 (    5)
  SS BOND              : angle       2.52055 (   10)
  hydrogen bonds       : bond        0.03507 (  407)
  hydrogen bonds       : angle       4.55620 ( 1158)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 HIS cc_start: 0.8165 (t70) cc_final: 0.7426 (t70)
REVERT: A  200 ASP cc_start: 0.7844 (m-30) cc_final: 0.7387 (t0)
REVERT: A  266 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6320 (mp)
REVERT: A  318 GLU cc_start: 0.6339 (tt0) cc_final: 0.6091 (tp30)
REVERT: A  333 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7852 (tp40)
REVERT: B   76 ASP cc_start: 0.7431 (t0) cc_final: 0.7048 (t70)
REVERT: B  164 THR cc_start: 0.6608 (p) cc_final: 0.6297 (p)
REVERT: C   21 MET cc_start: 0.8830 (mmm) cc_final: 0.8497 (tpp)
REVERT: E   65 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7338 (tppt)
REVERT: E  174 GLN cc_start: 0.7764 (tt0) cc_final: 0.7386 (mm-40)
REVERT: E  183 LEU cc_start: 0.7646 (mt) cc_final: 0.7333 (mp)
REVERT: R   46 LEU cc_start: 0.7584 (mt) cc_final: 0.7028 (pp)
REVERT: R   53 ARG cc_start: 0.5955 (ttp80) cc_final: 0.5242 (mpt180)
REVERT: R  106 MET cc_start: 0.7049 (mmp) cc_final: 0.6817 (mmm)
REVERT: R  138 TYR cc_start: 0.7572 (m-80) cc_final: 0.7230 (m-10)
REVERT: R  215 LYS cc_start: 0.7950 (tttt) cc_final: 0.7448 (mtmm)
  outliers start: 30
  outliers final: 27
  residues processed: 189
  average time/residue: 0.1172
  time to fit residues: 29.5287
Evaluate side-chains
  189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  147 CYS
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain R residue   61 VAL
Chi-restraints excluded: chain R residue   76 VAL
Chi-restraints excluded: chain R residue  122 CYS
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  155 SER
Chi-restraints excluded: chain R residue  180 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0870
   chunk 94 optimal weight:    0.5980
   chunk 50 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0010
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.3964

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.194130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.149009 restraints weight = 11167.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.87
r_work: 0.3657 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8919  Z= 0.119
  Angle     :  0.658  11.128  12070  Z= 0.328
  Chirality :  0.042   0.189   1353
  Planarity :  0.004   0.046   1515
  Dihedral  :  4.558  31.056   1198
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 22.25 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.27), residues: 1083
  helix:  1.94 (0.28), residues: 366
  sheet: -0.73 (0.33), residues: 268
  loop : -0.83 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 242 
 TYR   0.018   0.001   TYR R 185 
 PHE   0.019   0.001   PHE A 250 
 TRP   0.021   0.001   TRP R  93 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8914)
  covalent geometry    : angle       0.65508 (12060)
  SS BOND              : bond        0.00412 (    5)
  SS BOND              : angle       2.30706 (   10)
  hydrogen bonds       : bond        0.03286 (  407)
  hydrogen bonds       : angle       4.50910 ( 1158)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2377.51 seconds
wall clock time: 41 minutes 34.36 seconds (2494.36 seconds total)