Starting phenix.real_space_refine
on Tue Nov 18 03:16:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bx3_7303/11_2025/6bx3_7303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bx3_7303/11_2025/6bx3_7303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bx3_7303/11_2025/6bx3_7303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bx3_7303/11_2025/6bx3_7303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bx3_7303/11_2025/6bx3_7303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bx3_7303/11_2025/6bx3_7303.cif"
  }
  resolution = 4.3
  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=   0.001 sd=   0.030
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      47      5.16       5
     C    6608      2.51       5
     N    1786      2.21       5
     O    2015      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10456
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "E"
      Number of atoms: 1432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1432
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 6, 'TRANS': 185}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 72
    Chain: "K"
      Number of atoms: 1520
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1520
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 148
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 70
    Chain: "M"
      Number of atoms: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 328
          Classifications: {'peptide': 42}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 3, 'TRANS': 38}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 304
          Classifications: {'peptide': 40}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 36}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "F"
      Number of atoms: 1526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1526
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 68}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 280
          Unresolved non-hydrogen angles: 346
          Unresolved non-hydrogen dihedrals: 236
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 9, 'PHE:plan': 3, 'ASP:plan': 8, 'TRP:plan': 1, 'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 168
    Chain: "B"
      Number of atoms: 3050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3050
          Classifications: {'peptide': 399}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 16, 'TRANS': 382}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 196
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 14, 'GLN:plan1': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 107
    Chain: "A"
      Number of atoms: 2296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2296
          Classifications: {'peptide': 314}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 11, 'TRANS': 302}
          Unresolved non-hydrogen bonds: 138
          Unresolved non-hydrogen angles: 179
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 76
  Time building chain proxies: 2.67, per 1000 atoms: 0.26
  Number of scatterers: 10456
  At special positions: 0
  Unit cell: (137, 109, 155, 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      47     16.00
     O    2015      8.00
     N    1786      7.00
     C    6608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 392.2 milliseconds
  

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2658

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 15 sheets defined
      19.6% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'E' and resid 799 through 824
      removed outlier: 4.384A  pdb=" N   ARG E 805 " --> pdb=" O   TRP E 801 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   SER E 814 " --> pdb=" O   GLU E 810 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ASP E 815 " --> pdb=" O   GLU E 811 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN E 817 " --> pdb=" O   ALA E 813 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ILE E 818 " --> pdb=" O   SER E 814 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU E 824 " --> pdb=" O   LEU E 820 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 926 through 933
    Processing helix  chain 'E' and resid 974 through 988
      removed outlier: 3.570A  pdb=" N   ASN E 987 " --> pdb=" O   ARG E 983 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 98 through 106
      removed outlier: 3.659A  pdb=" N   LEU K 101 " --> pdb=" O   SER K  98 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER K 102 " --> pdb=" O   GLU K  99 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE K 103 " --> pdb=" O   GLY K 100 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   SER K 104 " --> pdb=" O   LEU K 101 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 196 through 200
    Processing helix  chain 'K' and resid 459 through 463
      removed outlier: 3.704A  pdb=" N   GLN K 462 " --> pdb=" O   TYR K 459 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 479 through 500
      removed outlier: 3.747A  pdb=" N   LYS K 483 " --> pdb=" O   ASP K 479 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 133 through 144
    Processing helix  chain 'M' and resid 152 through 162
      removed outlier: 3.523A  pdb=" N   LEU M 157 " --> pdb=" O   LEU M 153 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 123 through 129
    Processing helix  chain 'N' and resid 130 through 142
      removed outlier: 4.278A  pdb=" N   LEU N 134 " --> pdb=" O   VAL N 130 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 152 through 159
      removed outlier: 3.726A  pdb=" N   TYR N 156 " --> pdb=" O   VAL N 152 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 118 through 129
    Processing helix  chain 'F' and resid 135 through 145
      removed outlier: 3.574A  pdb=" N   GLU F 143 " --> pdb=" O   LYS F 139 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 150 through 158
      removed outlier: 3.858A  pdb=" N   PHE F 154 " --> pdb=" O   LYS F 150 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 164 through 171
      removed outlier: 3.653A  pdb=" N   ASP F 169 " --> pdb=" O   VAL F 165 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 191 through 200
      removed outlier: 4.713A  pdb=" N   GLU F 197 " --> pdb=" O   GLN F 193 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE F 198 " --> pdb=" O   GLU F 194 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU F 200 " --> pdb=" O   GLN F 196 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 208
    Processing helix  chain 'F' and resid 208 through 241
      removed outlier: 4.844A  pdb=" N   LEU F 217 " --> pdb=" O   TYR F 213 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ASP F 218 " --> pdb=" O   LEU F 214 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASP F 228 " --> pdb=" O   MET F 224 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ASP F 229 " --> pdb=" O   ARG F 225 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASP F 230 " --> pdb=" O   LYS F 226 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL F 235 " --> pdb=" O   ALA F 231 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 278 through 283
    Processing helix  chain 'F' and resid 311 through 349
      removed outlier: 3.698A  pdb=" N   TYR F 315 " --> pdb=" O   ASN F 311 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE F 342 " --> pdb=" O   LYS F 338 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TYR F 344 " --> pdb=" O   LEU F 340 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU F 349 " --> pdb=" O   TYR F 345 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 1023 through 1026
      removed outlier: 6.424A  pdb=" N   THR E1024 " --> pdb=" O   TYR E1039 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL E1037 " --> pdb=" O   LYS E1026 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 137 through 139
    Processing sheet with id=AA3, first strand: chain 'K' and resid 204 through 205
    Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23
      removed outlier: 4.321A  pdb=" N   ASP B 317 " --> pdb=" O   ASN B 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 34
      removed outlier: 5.318A  pdb=" N   CYS B  31 " --> pdb=" O   GLY B  44 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLY B  44 " --> pdb=" O   CYS B  31 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 79 through 80
      removed outlier: 3.683A  pdb=" N   LEU B  98 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS B 109 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122
      removed outlier: 4.097A  pdb=" N   TYR B 141 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 176
      removed outlier: 5.456A  pdb=" N   CYS B 174 " --> pdb=" O   GLY B 187 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLY B 187 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   LEU B 193 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   SER B 209 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   PHE B 195 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 269 through 274
      removed outlier: 6.431A  pdb=" N   SER B 285 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   ILE B 272 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   VAL B 283 " --> pdb=" O   ILE B 272 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   PHE B 274 " --> pdb=" O   TYR B 281 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   TYR B 281 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 61 through 62
      removed outlier: 4.263A  pdb=" N   ALA A  71 " --> pdb=" O   CYS A  62 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 102 through 104
      removed outlier: 3.947A  pdb=" N   THR A 103 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE A 112 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS A 121 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ILE A 120 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   THR A 133 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ILE A 122 " --> pdb=" O   MET A 131 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET A 131 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 141 through 143
    Processing sheet with id=AB4, first strand: chain 'A' and resid 162 through 163
    Processing sheet with id=AB5, first strand: chain 'A' and resid 204 through 207
      removed outlier: 3.686A  pdb=" N   LEU A 204 " --> pdb=" O   TRP A 216 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A 206 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL A 213 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   THR A 226 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ILE A 215 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 248 through 250

    223 hydrogen bonds defined for protein.
    627 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: 1.46

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2172
        1.33 -     1.45: 2588
        1.45 -     1.58: 5836
        1.58 -     1.70: 0
        1.70 -     1.83: 62
  Bond restraints: 10658
  Sorted by residual:
  bond pdb=" CA  HIS A  90 "
       pdb=" CB  HIS A  90 "
    ideal  model  delta    sigma   weight residual
    1.523  1.438  0.085 1.35e-02 5.49e+03 4.00e+01
  bond pdb=" C   THR N 131 "
       pdb=" N   PRO N 132 "
    ideal  model  delta    sigma   weight residual
    1.336  1.386 -0.050 1.20e-02 6.94e+03 1.76e+01
  bond pdb=" C   ALA E 943 "
       pdb=" O   ALA E 943 "
    ideal  model  delta    sigma   weight residual
    1.234  1.200  0.034 1.24e-02 6.50e+03 7.42e+00
  bond pdb=" CB  TRP A 312 "
       pdb=" CG  TRP A 312 "
    ideal  model  delta    sigma   weight residual
    1.498  1.415  0.083 3.10e-02 1.04e+03 7.11e+00
  bond pdb=" N   SER K 102 "
       pdb=" CA  SER K 102 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.20e-02 6.94e+03 6.89e+00
  ... (remaining 10653 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 13799
        3.04 -     6.08: 585
        6.08 -     9.12: 105
        9.12 -    12.16: 24
       12.16 -    15.19: 6
  Bond angle restraints: 14519
  Sorted by residual:
  angle pdb=" N   ILE E 972 "
        pdb=" CA  ILE E 972 "
        pdb=" C   ILE E 972 "
      ideal   model   delta    sigma   weight residual
     110.72  124.94  -14.22 1.01e+00 9.80e-01 1.98e+02
  angle pdb=" N   ALA B 350 "
        pdb=" CA  ALA B 350 "
        pdb=" C   ALA B 350 "
      ideal   model   delta    sigma   weight residual
     111.07  123.29  -12.22 1.07e+00 8.73e-01 1.30e+02
  angle pdb=" C   ASN B  25 "
        pdb=" N   PRO B  26 "
        pdb=" CA  PRO B  26 "
      ideal   model   delta    sigma   weight residual
     119.05  131.02  -11.97 1.11e+00 8.12e-01 1.16e+02
  angle pdb=" N   GLU B 356 "
        pdb=" CA  GLU B 356 "
        pdb=" C   GLU B 356 "
      ideal   model   delta    sigma   weight residual
     109.59   94.40   15.19 1.47e+00 4.63e-01 1.07e+02
  angle pdb=" C   LYS B 103 "
        pdb=" N   PRO B 104 "
        pdb=" CA  PRO B 104 "
      ideal   model   delta    sigma   weight residual
     119.87  129.81   -9.94 1.04e+00 9.25e-01 9.13e+01
  ... (remaining 14514 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.94: 5702
       14.94 -    29.87: 484
       29.87 -    44.81: 97
       44.81 -    59.74: 19
       59.74 -    74.68: 11
  Dihedral angle restraints: 6313
    sinusoidal: 2210
      harmonic: 4103
  Sorted by residual:
  dihedral pdb=" CA  HIS A 286 "
           pdb=" C   HIS A 286 "
           pdb=" N   SER A 287 "
           pdb=" CA  SER A 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -120.35  -59.65     0      5.00e+00 4.00e-02 1.42e+02
  dihedral pdb=" CA  ASN B  66 "
           pdb=" C   ASN B  66 "
           pdb=" N   MET B  67 "
           pdb=" CA  MET B  67 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -125.42  -54.58     0      5.00e+00 4.00e-02 1.19e+02
  dihedral pdb=" CA  ILE E 947 "
           pdb=" C   ILE E 947 "
           pdb=" N   HIS E 948 "
           pdb=" CA  HIS E 948 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -127.07  -52.93     0      5.00e+00 4.00e-02 1.12e+02
  ... (remaining 6310 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1420
       0.098 -    0.196: 218
       0.196 -    0.294: 33
       0.294 -    0.392: 12
       0.392 -    0.490: 3
  Chirality restraints: 1686
  Sorted by residual:
  chirality pdb=" CB  THR K 439 "
            pdb=" CA  THR K 439 "
            pdb=" OG1 THR K 439 "
            pdb=" CG2 THR K 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.06    0.49 2.00e-01 2.50e+01 5.99e+00
  chirality pdb=" CG  LEU B 154 "
            pdb=" CB  LEU B 154 "
            pdb=" CD1 LEU B 154 "
            pdb=" CD2 LEU B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.18   -0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" CA  PRO B  26 "
            pdb=" N   PRO B  26 "
            pdb=" C   PRO B  26 "
            pdb=" CB  PRO B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.33    0.39 2.00e-01 2.50e+01 3.84e+00
  ... (remaining 1683 not shown)

  Planarity restraints: 1879
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 164 "   -0.022 2.00e-02 2.50e+03   4.44e-02 1.97e+01
        pdb=" C   ILE F 164 "    0.077 2.00e-02 2.50e+03
        pdb=" O   ILE F 164 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   VAL F 165 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 113 "    0.020 2.00e-02 2.50e+03   4.07e-02 1.65e+01
        pdb=" C   PHE B 113 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PHE B 113 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ASP B 114 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 943 "   -0.018 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   ALA E 943 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ALA E 943 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ARG E 944 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1876 not shown)

  Histogram of nonbonded interaction distances:
        1.09 -     1.86: 3
        1.86 -     2.62: 230
        2.62 -     3.38: 14421
        3.38 -     4.14: 24674
        4.14 -     4.90: 41121
  Nonbonded interactions: 80449
  Sorted by model distance:
  nonbonded pdb=" CB  ASP K 125 "
            pdb=" OH  TYR K 482 "
     model   vdw
     1.094 3.440
  nonbonded pdb=" O   CYS F 263 "
            pdb=" OG1 THR F 297 "
     model   vdw
     1.520 3.040
  nonbonded pdb=" CB  ASP K 125 "
            pdb=" CZ  TYR K 482 "
     model   vdw
     1.775 3.660
  nonbonded pdb=" O   ASP K  96 "
            pdb=" CB  ARG K 123 "
     model   vdw
     1.917 3.440
  nonbonded pdb=" CG2 THR F 297 "
            pdb=" CE1 HIS F 304 "
     model   vdw
     1.955 3.680
  ... (remaining 80444 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'M' and (resid 122 through 138 or (resid 139 through 140 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 141 through 146 or (resid 147  \ 
and (name N or name CA or name C or name O or name CB )) or resid 148 through 16 \ 
1))
  selection = (chain 'N' and (resid 122 through 125 or (resid 126 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 127 through 142 or (resid 143 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 144 through 161))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.07 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.820
  Find NCS groups from input model:        0.060
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085  10658  Z= 0.397
  Angle     :  1.492  15.194  14519  Z= 0.898
  Chirality :  0.079   0.490   1686
  Planarity :  0.008   0.072   1879
  Dihedral  : 12.650  74.679   3655
  Min Nonbonded Distance : 1.094

Molprobity Statistics.
  All-atom Clashscore : 24.93
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 18.77 %
    Favored  : 81.16 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.17 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.17 %
    Twisted General : 1.26 %

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 are not related in a simple way.
  whole: -5.00 (0.17), residues: 1385
  helix: -2.80 (0.24), residues: 229
  sheet: -2.94 (0.34), residues: 173
  loop : -3.83 (0.15), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 841 
 TYR   0.031   0.004   TYR K 202 
 PHE   0.030   0.004   PHE F 283 
 TRP   0.033   0.004   TRP K 135 
 HIS   0.015   0.003   HIS A 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00743 (10658)
  covalent geometry    : angle       1.49184 (14519)
  hydrogen bonds       : bond        0.21959 (  223)
  hydrogen bonds       : angle       8.86331 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 283
  time to evaluate  : 0.362 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  819 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9167 (mm-30)
REVERT: E  934 ASN cc_start: 0.9318 (t160) cc_final: 0.8889 (p0)
REVERT: E  975 PRO cc_start: 0.8494 (Cg_exo) cc_final: 0.8142 (Cg_endo)
REVERT: E  979 MET cc_start: 0.8978 (tpt) cc_final: 0.8649 (tpp)
REVERT: E  998 ASP cc_start: 0.7816 (m-30) cc_final: 0.6240 (p0)
REVERT: E 1026 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8197 (mtmm)
REVERT: E 1039 TYR cc_start: 0.8089 (t80) cc_final: 0.7490 (t80)
REVERT: K  194 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8301 (tm-30)
REVERT: K  199 PHE cc_start: 0.9470 (t80) cc_final: 0.8995 (t80)
REVERT: K  469 VAL cc_start: 0.6236 (t) cc_final: 0.5743 (t)
REVERT: K  483 LYS cc_start: 0.9018 (mptt) cc_final: 0.8808 (mmtt)
REVERT: M  139 ARG cc_start: 0.8745 (mmp-170) cc_final: 0.7931 (mtt180)
REVERT: M  147 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7057 (mp0)
REVERT: N  123 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7781 (mtt180)
REVERT: F  120 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8239 (mm-30)
REVERT: F  204 LYS cc_start: 0.9089 (ttpm) cc_final: 0.8748 (ptpp)
REVERT: F  223 GLU cc_start: 0.9661 (tt0) cc_final: 0.9441 (tm-30)
REVERT: F  228 ASP cc_start: 0.8918 (m-30) cc_final: 0.8712 (t0)
REVERT: F  291 LYS cc_start: 0.8185 (pttp) cc_final: 0.7087 (mmmt)
REVERT: B   54 ASP cc_start: 0.8339 (p0) cc_final: 0.7376 (p0)
REVERT: B   59 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.8389 (mmm-85)
REVERT: B   67 MET cc_start: 0.9076 (mpm) cc_final: 0.8741 (mmm)
REVERT: B  144 ASP cc_start: 0.9572 (m-30) cc_final: 0.9095 (t70)
REVERT: B  258 HIS cc_start: 0.7965 (t-90) cc_final: 0.7657 (t-170)
REVERT: B  268 GLN cc_start: 0.8249 (pp30) cc_final: 0.8007 (pp30)
REVERT: B  319 ASN cc_start: 0.9046 (t0) cc_final: 0.8765 (t0)
REVERT: B  320 TRP cc_start: 0.8524 (m100) cc_final: 0.8266 (m100)
REVERT: B  354 ASP cc_start: 0.8753 (m-30) cc_final: 0.7945 (t0)
REVERT: A  116 MET cc_start: 0.7837 (tmt) cc_final: 0.7478 (tmm)
REVERT: A  127 ASN cc_start: 0.9137 (t160) cc_final: 0.8850 (t0)
REVERT: A  149 ASN cc_start: 0.9139 (m-40) cc_final: 0.8873 (m-40)
REVERT: A  196 LYS cc_start: 0.8564 (tttp) cc_final: 0.8238 (ttmm)
REVERT: A  249 GLU cc_start: 0.7906 (mp0) cc_final: 0.7592 (mp0)
REVERT: A  291 MET cc_start: 0.8426 (tpp) cc_final: 0.7926 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 291
  average time/residue: 0.1142
  time to fit residues: 45.7269
Evaluate side-chains
  176 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 172
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    0.0010
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    3.5994

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

Flipped N/Q/H residues before XYZ refinement:
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 215 HIS
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 145 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 193 GLN
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 343 GLN
B   6 GLN
** B  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 ASN
B 330 ASN
A 127 ASN
A 172 HIS
A 294 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.078260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.066494 restraints weight = 61877.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.068298 restraints weight = 41223.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.069600 restraints weight = 30218.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.070551 restraints weight = 23646.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.071268 restraints weight = 19428.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3533 r_free = 0.3533    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10658  Z= 0.227
  Angle     :  0.894  15.957  14519  Z= 0.471
  Chirality :  0.052   0.303   1686
  Planarity :  0.005   0.049   1879
  Dihedral  :  8.835  48.191   1491
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 21.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.33 %
    Favored  : 82.67 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.54 %
    Favored  : 95.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.67 %

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 are not related in a simple way.
  whole: -4.45 (0.19), residues: 1385
  helix: -1.97 (0.27), residues: 255
  sheet: -2.96 (0.33), residues: 183
  loop : -3.49 (0.17), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 841 
 TYR   0.023   0.002   TYR M 156 
 PHE   0.021   0.002   PHE B 355 
 TRP   0.024   0.002   TRP K 135 
 HIS   0.011   0.002   HIS A  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 (10658)
  covalent geometry    : angle       0.89411 (14519)
  hydrogen bonds       : bond        0.05055 (  223)
  hydrogen bonds       : angle       6.51640 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 227
  time to evaluate  : 0.429 
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: symmetry clash
   revert: symmetry clash
REVERT: E  934 ASN cc_start: 0.9204 (t0) cc_final: 0.8896 (p0)
REVERT: E  998 ASP cc_start: 0.7511 (m-30) cc_final: 0.6672 (m-30)
REVERT: K  135 TRP cc_start: 0.8688 (t60) cc_final: 0.8314 (t60)
REVERT: K  194 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8172 (tm-30)
REVERT: K  483 LYS cc_start: 0.9290 (mptt) cc_final: 0.8619 (mtpt)
REVERT: M  139 ARG cc_start: 0.8852 (mmp-170) cc_final: 0.8080 (mtt180)
REVERT: F  266 CYS cc_start: 0.8211 (p) cc_final: 0.7964 (p)
REVERT: F  291 LYS cc_start: 0.7876 (pttp) cc_final: 0.6661 (mmmt)
REVERT: B   83 ASP cc_start: 0.8185 (t0) cc_final: 0.7819 (t0)
REVERT: B  106 LYS cc_start: 0.8713 (tttp) cc_final: 0.8389 (mtmm)
REVERT: B  319 ASN cc_start: 0.9100 (t0) cc_final: 0.8844 (t0)
REVERT: B  320 TRP cc_start: 0.8392 (m100) cc_final: 0.8042 (m100)
REVERT: B  354 ASP cc_start: 0.8981 (m-30) cc_final: 0.7951 (t0)
REVERT: A   26 GLN cc_start: 0.9094 (mp10) cc_final: 0.8873 (mp10)
REVERT: A  149 ASN cc_start: 0.9193 (m-40) cc_final: 0.8731 (m-40)
REVERT: A  154 LEU cc_start: 0.8723 (tp) cc_final: 0.8275 (tp)
REVERT: A  194 GLN cc_start: 0.8882 (mt0) cc_final: 0.8644 (mt0)
REVERT: A  195 VAL cc_start: 0.8460 (m) cc_final: 0.7607 (p)
REVERT: A  199 GLU cc_start: 0.8588 (pm20) cc_final: 0.8313 (pm20)
REVERT: A  233 GLU cc_start: 0.7658 (tp30) cc_final: 0.7337 (tp30)
REVERT: A  291 MET cc_start: 0.8366 (tpp) cc_final: 0.7505 (mmp)
  outliers start: 3
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1049
  time to fit residues: 34.1491
Evaluate side-chains
  153 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 52 optimal weight:    0.0020
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 137 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E1022 ASN
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
B 336 ASN
A 109 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.081314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.069109 restraints weight = 59332.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.071073 restraints weight = 38051.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.072512 restraints weight = 27136.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.073571 restraints weight = 20829.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.074350 restraints weight = 16840.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10658  Z= 0.140
  Angle     :  0.781  10.845  14519  Z= 0.404
  Chirality :  0.050   0.280   1686
  Planarity :  0.004   0.042   1879
  Dihedral  :  7.774  43.053   1491
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 16.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.17 %
    Favored  : 83.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

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 are not related in a simple way.
  whole: -3.94 (0.20), residues: 1385
  helix: -1.00 (0.31), residues: 249
  sheet: -2.85 (0.37), residues: 148
  loop : -3.28 (0.17), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 980 
 TYR   0.018   0.002   TYR B  40 
 PHE   0.029   0.002   PHE E 835 
 TRP   0.016   0.002   TRP K 135 
 HIS   0.006   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10658)
  covalent geometry    : angle       0.78149 (14519)
  hydrogen bonds       : bond        0.04112 (  223)
  hydrogen bonds       : angle       5.88315 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.429 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  934 ASN cc_start: 0.9155 (t0) cc_final: 0.8848 (p0)
REVERT: E  975 PRO cc_start: 0.8354 (Cg_exo) cc_final: 0.8141 (Cg_endo)
REVERT: E  979 MET cc_start: 0.8840 (tpt) cc_final: 0.8565 (tpp)
REVERT: K  117 TYR cc_start: 0.5471 (m-10) cc_final: 0.5064 (m-80)
REVERT: K  199 PHE cc_start: 0.9089 (t80) cc_final: 0.8848 (t80)
REVERT: K  238 LEU cc_start: 0.8729 (tp) cc_final: 0.8514 (tp)
REVERT: M  139 ARG cc_start: 0.8902 (mmp-170) cc_final: 0.8194 (mtt180)
REVERT: M  156 TYR cc_start: 0.8556 (t80) cc_final: 0.7851 (t80)
REVERT: F  266 CYS cc_start: 0.8470 (p) cc_final: 0.8175 (p)
REVERT: F  291 LYS cc_start: 0.7786 (pttp) cc_final: 0.6431 (mmmt)
REVERT: B   54 ASP cc_start: 0.8333 (p0) cc_final: 0.7435 (p0)
REVERT: B  199 HIS cc_start: 0.6548 (t70) cc_final: 0.6157 (t70)
REVERT: B  354 ASP cc_start: 0.8993 (m-30) cc_final: 0.7409 (t0)
REVERT: A   26 GLN cc_start: 0.9158 (mp10) cc_final: 0.8882 (mp10)
REVERT: A  107 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8665 (mtpt)
REVERT: A  109 ASN cc_start: 0.9286 (m110) cc_final: 0.8738 (m-40)
REVERT: A  149 ASN cc_start: 0.9195 (m-40) cc_final: 0.8696 (m-40)
REVERT: A  195 VAL cc_start: 0.8471 (m) cc_final: 0.7562 (p)
REVERT: A  199 GLU cc_start: 0.8572 (pm20) cc_final: 0.8274 (pm20)
REVERT: A  238 HIS cc_start: 0.7496 (p-80) cc_final: 0.7023 (p-80)
REVERT: A  291 MET cc_start: 0.8218 (tpp) cc_final: 0.7084 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.0976
  time to fit residues: 32.5621
Evaluate side-chains
  160 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 43 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 106 optimal weight:    8.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.077179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.065493 restraints weight = 61690.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.067220 restraints weight = 41124.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.068482 restraints weight = 30160.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.069384 restraints weight = 23756.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.070078 restraints weight = 19644.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.4200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  10658  Z= 0.232
  Angle     :  0.836  11.343  14519  Z= 0.441
  Chirality :  0.050   0.256   1686
  Planarity :  0.005   0.045   1879
  Dihedral  :  7.812  43.559   1491
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 22.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.40 %
    Favored  : 82.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

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 are not related in a simple way.
  whole: -3.94 (0.20), residues: 1385
  helix: -1.08 (0.30), residues: 248
  sheet: -2.82 (0.40), residues: 140
  loop : -3.26 (0.17), residues: 997

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 841 
 TYR   0.027   0.002   TYR F 213 
 PHE   0.027   0.002   PHE B  58 
 TRP   0.026   0.003   TRP E 950 
 HIS   0.012   0.002   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (10658)
  covalent geometry    : angle       0.83559 (14519)
  hydrogen bonds       : bond        0.04329 (  223)
  hydrogen bonds       : angle       5.83241 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.455 
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: symmetry clash
   revert: symmetry clash
REVERT: E  934 ASN cc_start: 0.9099 (t0) cc_final: 0.8793 (p0)
REVERT: K  135 TRP cc_start: 0.8827 (t60) cc_final: 0.8512 (t60)
REVERT: K  194 GLU cc_start: 0.8443 (mp0) cc_final: 0.7973 (tm-30)
REVERT: K  483 LYS cc_start: 0.9192 (mptt) cc_final: 0.8593 (mttm)
REVERT: M  139 ARG cc_start: 0.8911 (mmp-170) cc_final: 0.8258 (mtt180)
REVERT: F  266 CYS cc_start: 0.8599 (p) cc_final: 0.8326 (p)
REVERT: F  291 LYS cc_start: 0.7922 (pttp) cc_final: 0.6618 (mmmt)
REVERT: B  347 LYS cc_start: 0.8414 (mttt) cc_final: 0.8168 (mppt)
REVERT: B  354 ASP cc_start: 0.8951 (m-30) cc_final: 0.7784 (t0)
REVERT: A   26 GLN cc_start: 0.9135 (mp10) cc_final: 0.8914 (mp10)
REVERT: A  107 LYS cc_start: 0.9345 (mtpt) cc_final: 0.8682 (mtpt)
REVERT: A  109 ASN cc_start: 0.9340 (m110) cc_final: 0.8710 (m-40)
REVERT: A  149 ASN cc_start: 0.9135 (m-40) cc_final: 0.8648 (m-40)
REVERT: A  195 VAL cc_start: 0.8690 (m) cc_final: 0.7956 (p)
REVERT: A  291 MET cc_start: 0.8318 (tpp) cc_final: 0.7243 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1019
  time to fit residues: 27.7496
Evaluate side-chains
  137 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 48 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 99 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 932 GLN
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 225 ASN
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 330 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.081128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.069287 restraints weight = 60664.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.071083 restraints weight = 40222.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.072409 restraints weight = 29402.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.073374 restraints weight = 23006.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.074079 restraints weight = 18919.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.4557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10658  Z= 0.132
  Angle     :  0.758   9.893  14519  Z= 0.391
  Chirality :  0.049   0.241   1686
  Planarity :  0.004   0.034   1879
  Dihedral  :  7.232  40.515   1491
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 15.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.31 %
    Favored  : 84.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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 are not related in a simple way.
  whole: -3.69 (0.20), residues: 1385
  helix: -0.62 (0.33), residues: 243
  sheet: -2.49 (0.39), residues: 149
  loop : -3.18 (0.17), residues: 993

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG M 151 
 TYR   0.023   0.002   TYR A 260 
 PHE   0.025   0.002   PHE K 358 
 TRP   0.022   0.002   TRP A 183 
 HIS   0.007   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10658)
  covalent geometry    : angle       0.75757 (14519)
  hydrogen bonds       : bond        0.03735 (  223)
  hydrogen bonds       : angle       5.48751 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.418 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  815 ASP cc_start: 0.8943 (t0) cc_final: 0.8292 (t0)
REVERT: E  819 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8860 (mm-30)
REVERT: K  117 TYR cc_start: 0.5402 (m-10) cc_final: 0.5194 (m-80)
REVERT: K  194 GLU cc_start: 0.8266 (mp0) cc_final: 0.7800 (tm-30)
REVERT: K  483 LYS cc_start: 0.9165 (mptt) cc_final: 0.8429 (mttm)
REVERT: M  139 ARG cc_start: 0.8896 (mmp-170) cc_final: 0.8206 (mtt180)
REVERT: M  156 TYR cc_start: 0.8499 (t80) cc_final: 0.8120 (t80)
REVERT: M  160 GLN cc_start: 0.7038 (tt0) cc_final: 0.6226 (tp40)
REVERT: F  224 MET cc_start: 0.8595 (mmm) cc_final: 0.8333 (mmm)
REVERT: F  269 TYR cc_start: 0.7623 (p90) cc_final: 0.7360 (p90)
REVERT: F  291 LYS cc_start: 0.7724 (pttp) cc_final: 0.7315 (pttm)
REVERT: B   54 ASP cc_start: 0.8292 (p0) cc_final: 0.7291 (p0)
REVERT: B   83 ASP cc_start: 0.8144 (t0) cc_final: 0.7774 (t0)
REVERT: B  354 ASP cc_start: 0.8929 (m-30) cc_final: 0.7955 (t0)
REVERT: A   26 GLN cc_start: 0.8999 (mp10) cc_final: 0.8709 (mp10)
REVERT: A   54 HIS cc_start: 0.6977 (m90) cc_final: 0.6760 (m-70)
REVERT: A  107 LYS cc_start: 0.9341 (mtpt) cc_final: 0.8670 (mtpt)
REVERT: A  109 ASN cc_start: 0.9266 (m110) cc_final: 0.8725 (m-40)
REVERT: A  149 ASN cc_start: 0.9191 (m-40) cc_final: 0.8703 (m-40)
REVERT: A  155 SER cc_start: 0.7236 (p) cc_final: 0.6982 (p)
REVERT: A  195 VAL cc_start: 0.8576 (m) cc_final: 0.7812 (p)
REVERT: A  233 GLU cc_start: 0.8090 (tp30) cc_final: 0.7772 (tp30)
REVERT: A  241 CYS cc_start: 0.8155 (p) cc_final: 0.7421 (m)
REVERT: A  291 MET cc_start: 0.8144 (tpp) cc_final: 0.6866 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.0991
  time to fit residues: 30.9715
Evaluate side-chains
  149 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 74 optimal weight:    0.7980
   chunk 96 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 107 optimal weight:   20.0000
   chunk 72 optimal weight:    4.9990
   chunk 18 optimal weight:   20.0000
   chunk 112 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E1022 ASN
K 444 ASN
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 330 ASN
A 127 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.079596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.067841 restraints weight = 62426.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.069593 restraints weight = 41635.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.070888 restraints weight = 30552.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.071841 restraints weight = 23946.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.072543 restraints weight = 19721.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.4793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10658  Z= 0.159
  Angle     :  0.753  10.068  14519  Z= 0.389
  Chirality :  0.048   0.238   1686
  Planarity :  0.004   0.042   1879
  Dihedral  :  7.109  39.762   1491
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.47 %
    Favored  : 82.53 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.38 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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 are not related in a simple way.
  whole: -3.66 (0.20), residues: 1385
  helix: -0.57 (0.32), residues: 244
  sheet: -2.37 (0.39), residues: 154
  loop : -3.20 (0.17), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 106 
 TYR   0.018   0.002   TYR B 281 
 PHE   0.024   0.002   PHE B  58 
 TRP   0.020   0.002   TRP A 183 
 HIS   0.010   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10658)
  covalent geometry    : angle       0.75279 (14519)
  hydrogen bonds       : bond        0.03720 (  223)
  hydrogen bonds       : angle       5.40992 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.446 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  815 ASP cc_start: 0.8968 (t0) cc_final: 0.8308 (t0)
REVERT: E  819 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8848 (mm-30)
REVERT: K  117 TYR cc_start: 0.5527 (m-10) cc_final: 0.5297 (m-80)
REVERT: K  135 TRP cc_start: 0.8660 (t60) cc_final: 0.8237 (t60)
REVERT: K  194 GLU cc_start: 0.8353 (mp0) cc_final: 0.7803 (tm-30)
REVERT: K  444 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.5864 (p0)
REVERT: K  483 LYS cc_start: 0.9175 (mptt) cc_final: 0.8475 (mttm)
REVERT: M  135 LEU cc_start: 0.8698 (pp) cc_final: 0.8409 (pp)
REVERT: M  139 ARG cc_start: 0.8976 (mmp-170) cc_final: 0.8159 (mtt180)
REVERT: M  156 TYR cc_start: 0.8546 (t80) cc_final: 0.8327 (t80)
REVERT: F  199 SER cc_start: 0.9139 (t) cc_final: 0.8892 (m)
REVERT: F  269 TYR cc_start: 0.7816 (p90) cc_final: 0.7548 (p90)
REVERT: F  291 LYS cc_start: 0.7706 (pttp) cc_final: 0.6267 (mmmt)
REVERT: B   54 ASP cc_start: 0.8326 (p0) cc_final: 0.7364 (p0)
REVERT: B  354 ASP cc_start: 0.8912 (m-30) cc_final: 0.7790 (t0)
REVERT: A   26 GLN cc_start: 0.9061 (mp10) cc_final: 0.8819 (mp10)
REVERT: A   54 HIS cc_start: 0.7207 (m90) cc_final: 0.6721 (m-70)
REVERT: A   88 LEU cc_start: 0.6977 (tt) cc_final: 0.6688 (tt)
REVERT: A  107 LYS cc_start: 0.9313 (mtpt) cc_final: 0.8654 (mtpt)
REVERT: A  109 ASN cc_start: 0.9332 (m110) cc_final: 0.8786 (m-40)
REVERT: A  149 ASN cc_start: 0.9225 (m-40) cc_final: 0.8763 (m-40)
REVERT: A  155 SER cc_start: 0.7416 (p) cc_final: 0.7117 (p)
REVERT: A  195 VAL cc_start: 0.8567 (m) cc_final: 0.7853 (p)
REVERT: A  233 GLU cc_start: 0.8219 (tp30) cc_final: 0.7910 (tp30)
REVERT: A  241 CYS cc_start: 0.8181 (p) cc_final: 0.7419 (m)
REVERT: A  291 MET cc_start: 0.8175 (tpp) cc_final: 0.7112 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0931
  time to fit residues: 27.0566
Evaluate side-chains
  142 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0270
   chunk 113 optimal weight:    3.9990
   chunk 107 optimal weight:   30.0000
   chunk 12 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 124 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.5444

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

Flipped N/Q/H residues before XYZ refinement:
** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.080455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.068551 restraints weight = 61296.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.070405 restraints weight = 40131.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.071759 restraints weight = 29058.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.072759 restraints weight = 22481.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.073496 restraints weight = 18300.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.5054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10658  Z= 0.136
  Angle     :  0.747  10.605  14519  Z= 0.386
  Chirality :  0.048   0.247   1686
  Planarity :  0.004   0.036   1879
  Dihedral  :  6.926  37.978   1491
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.67 %
    Favored  : 84.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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 are not related in a simple way.
  whole: -3.52 (0.20), residues: 1385
  helix: -0.41 (0.33), residues: 245
  sheet: -2.04 (0.42), residues: 139
  loop : -3.16 (0.17), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 973 
 TYR   0.029   0.002   TYR F 213 
 PHE   0.025   0.002   PHE B  58 
 TRP   0.024   0.002   TRP A 183 
 HIS   0.008   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10658)
  covalent geometry    : angle       0.74736 (14519)
  hydrogen bonds       : bond        0.03618 (  223)
  hydrogen bonds       : angle       5.30138 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.395 
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: symmetry clash
   revert: symmetry clash
REVERT: E  825 PHE cc_start: 0.7060 (m-10) cc_final: 0.6676 (m-10)
REVERT: K  483 LYS cc_start: 0.9095 (mptt) cc_final: 0.8370 (mttm)
REVERT: M  135 LEU cc_start: 0.8666 (pp) cc_final: 0.8377 (pp)
REVERT: M  139 ARG cc_start: 0.9022 (mmp-170) cc_final: 0.8250 (mtt180)
REVERT: M  156 TYR cc_start: 0.8577 (t80) cc_final: 0.7985 (t80)
REVERT: M  160 GLN cc_start: 0.6710 (pt0) cc_final: 0.6493 (pt0)
REVERT: F  199 SER cc_start: 0.9071 (t) cc_final: 0.8841 (m)
REVERT: F  224 MET cc_start: 0.8648 (mmm) cc_final: 0.8384 (mmt)
REVERT: F  269 TYR cc_start: 0.7692 (p90) cc_final: 0.7460 (p90)
REVERT: F  291 LYS cc_start: 0.7628 (pttp) cc_final: 0.6152 (mmmt)
REVERT: B   54 ASP cc_start: 0.8336 (p0) cc_final: 0.7358 (p0)
REVERT: B  354 ASP cc_start: 0.8893 (m-30) cc_final: 0.7747 (t0)
REVERT: A   26 GLN cc_start: 0.8975 (mp10) cc_final: 0.8722 (mp10)
REVERT: A   54 HIS cc_start: 0.7110 (m90) cc_final: 0.6546 (m170)
REVERT: A  107 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8562 (mtpt)
REVERT: A  109 ASN cc_start: 0.9286 (m110) cc_final: 0.8757 (m-40)
REVERT: A  149 ASN cc_start: 0.9270 (m-40) cc_final: 0.8788 (m-40)
REVERT: A  195 VAL cc_start: 0.8670 (m) cc_final: 0.8222 (p)
REVERT: A  233 GLU cc_start: 0.8223 (tp30) cc_final: 0.7890 (tp30)
REVERT: A  241 CYS cc_start: 0.8157 (p) cc_final: 0.7474 (m)
REVERT: A  291 MET cc_start: 0.8127 (tpp) cc_final: 0.7080 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0921
  time to fit residues: 26.4567
Evaluate side-chains
  144 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 70 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   chunk 107 optimal weight:   30.0000
   chunk 36 optimal weight:    0.0070
   chunk 29 optimal weight:    0.2980
   chunk 104 optimal weight:    0.1980
   chunk 113 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    0.3398

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

Flipped N/Q/H residues before XYZ refinement:
E 821 ASN
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 196 GLN
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 258 HIS
B 330 ASN
A  95 HIS
A 127 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.082885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.070812 restraints weight = 62311.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.072683 restraints weight = 40880.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.074042 restraints weight = 29623.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.075057 restraints weight = 23022.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.075811 restraints weight = 18811.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.5381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10658  Z= 0.124
  Angle     :  0.743  10.913  14519  Z= 0.378
  Chirality :  0.048   0.252   1686
  Planarity :  0.004   0.039   1879
  Dihedral  :  6.547  36.566   1491
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.51 %
    Favored  : 85.42 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.25 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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 are not related in a simple way.
  whole: -3.44 (0.20), residues: 1385
  helix: -0.12 (0.34), residues: 238
  sheet: -2.15 (0.40), residues: 151
  loop : -3.12 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 973 
 TYR   0.013   0.001   TYR A 284 
 PHE   0.026   0.002   PHE B  58 
 TRP   0.028   0.002   TRP A 183 
 HIS   0.004   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (10658)
  covalent geometry    : angle       0.74269 (14519)
  hydrogen bonds       : bond        0.03333 (  223)
  hydrogen bonds       : angle       5.02210 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  825 PHE cc_start: 0.6854 (m-10) cc_final: 0.6570 (m-10)
REVERT: K  117 TYR cc_start: 0.5459 (m-10) cc_final: 0.5078 (m-10)
REVERT: K  483 LYS cc_start: 0.9080 (mptt) cc_final: 0.8340 (mttm)
REVERT: M  139 ARG cc_start: 0.9054 (mmp-170) cc_final: 0.8649 (mmt180)
REVERT: M  156 TYR cc_start: 0.8241 (t80) cc_final: 0.7588 (t80)
REVERT: M  160 GLN cc_start: 0.6618 (pt0) cc_final: 0.6309 (pt0)
REVERT: F  199 SER cc_start: 0.9016 (t) cc_final: 0.8685 (m)
REVERT: F  291 LYS cc_start: 0.7655 (pttp) cc_final: 0.6150 (mmmt)
REVERT: B   54 ASP cc_start: 0.8273 (p0) cc_final: 0.7294 (p0)
REVERT: B  199 HIS cc_start: 0.7333 (t70) cc_final: 0.6791 (t70)
REVERT: B  325 MET cc_start: 0.8752 (mmp) cc_final: 0.7360 (ppp)
REVERT: B  347 LYS cc_start: 0.8434 (mttt) cc_final: 0.8140 (mppt)
REVERT: B  354 ASP cc_start: 0.8901 (m-30) cc_final: 0.7720 (t0)
REVERT: A   42 ASN cc_start: 0.8900 (m-40) cc_final: 0.7897 (m110)
REVERT: A   54 HIS cc_start: 0.7053 (m90) cc_final: 0.6548 (m170)
REVERT: A  107 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8457 (mtpt)
REVERT: A  109 ASN cc_start: 0.9239 (m110) cc_final: 0.8722 (m-40)
REVERT: A  142 VAL cc_start: 0.9350 (p) cc_final: 0.9060 (m)
REVERT: A  195 VAL cc_start: 0.8621 (m) cc_final: 0.8252 (p)
REVERT: A  233 GLU cc_start: 0.8153 (tp30) cc_final: 0.7808 (tp30)
REVERT: A  241 CYS cc_start: 0.8179 (p) cc_final: 0.7464 (m)
REVERT: A  291 MET cc_start: 0.7966 (tpp) cc_final: 0.7014 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0883
  time to fit residues: 28.1433
Evaluate side-chains
  146 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 94 optimal weight:    0.2980
   chunk 66 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0010
   chunk 19 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 107 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0040
   chunk 63 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.3598

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

Flipped N/Q/H residues before XYZ refinement:
** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 258 HIS
B 330 ASN
A 127 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.083939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.072307 restraints weight = 62209.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.074131 restraints weight = 41580.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.075421 restraints weight = 30393.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.076392 restraints weight = 23776.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.077000 restraints weight = 19539.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.5708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10658  Z= 0.122
  Angle     :  0.730  10.995  14519  Z= 0.372
  Chirality :  0.047   0.258   1686
  Planarity :  0.004   0.054   1879
  Dihedral  :  6.341  34.513   1491
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.51 %
    Favored  : 85.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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 are not related in a simple way.
  whole: -3.36 (0.20), residues: 1385
  helix:  0.02 (0.34), residues: 239
  sheet: -2.28 (0.41), residues: 138
  loop : -3.06 (0.17), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  97 
 TYR   0.026   0.002   TYR F 213 
 PHE   0.026   0.001   PHE B  58 
 TRP   0.026   0.002   TRP A 183 
 HIS   0.007   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10658)
  covalent geometry    : angle       0.72985 (14519)
  hydrogen bonds       : bond        0.03206 (  223)
  hydrogen bonds       : angle       4.91198 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.428 
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: E  825 PHE cc_start: 0.6844 (m-10) cc_final: 0.6538 (m-10)
REVERT: K  483 LYS cc_start: 0.9100 (mptt) cc_final: 0.8363 (mttm)
REVERT: M  139 ARG cc_start: 0.8989 (mmp-170) cc_final: 0.8308 (mmt180)
REVERT: M  160 GLN cc_start: 0.6622 (pt0) cc_final: 0.5471 (tp40)
REVERT: F  199 SER cc_start: 0.8838 (t) cc_final: 0.8609 (m)
REVERT: F  213 TYR cc_start: 0.7469 (t80) cc_final: 0.6659 (t80)
REVERT: F  291 LYS cc_start: 0.7691 (pttp) cc_final: 0.6236 (mmmt)
REVERT: B   30 GLU cc_start: 0.7034 (tt0) cc_final: 0.6615 (tp30)
REVERT: B   54 ASP cc_start: 0.8195 (p0) cc_final: 0.7196 (p0)
REVERT: B   83 ASP cc_start: 0.7827 (t0) cc_final: 0.7493 (t0)
REVERT: B  199 HIS cc_start: 0.7351 (t70) cc_final: 0.6829 (t70)
REVERT: B  325 MET cc_start: 0.8659 (mmp) cc_final: 0.7459 (ppp)
REVERT: B  347 LYS cc_start: 0.8428 (mttt) cc_final: 0.8107 (mppt)
REVERT: B  354 ASP cc_start: 0.8877 (m-30) cc_final: 0.7762 (t0)
REVERT: A   42 ASN cc_start: 0.8825 (m-40) cc_final: 0.7868 (m110)
REVERT: A   54 HIS cc_start: 0.7114 (m90) cc_final: 0.6569 (m170)
REVERT: A  107 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8404 (mtpt)
REVERT: A  109 ASN cc_start: 0.9137 (m110) cc_final: 0.8697 (m110)
REVERT: A  195 VAL cc_start: 0.8623 (m) cc_final: 0.8347 (p)
REVERT: A  233 GLU cc_start: 0.8118 (tp30) cc_final: 0.7728 (tp30)
REVERT: A  241 CYS cc_start: 0.8048 (p) cc_final: 0.7237 (m)
REVERT: A  291 MET cc_start: 0.7914 (tpp) cc_final: 0.7026 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0894
  time to fit residues: 28.2778
Evaluate side-chains
  152 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 60 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 100 optimal weight:    0.0070
   chunk 21 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 90 optimal weight:   20.0000
   chunk 46 optimal weight:   20.0000
   chunk 4 optimal weight:    0.0470
   overall best weight:    1.8102

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

Flipped N/Q/H residues before XYZ refinement:
** E1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 258 HIS
B 330 ASN
A 127 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.081866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.070176 restraints weight = 62109.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.071956 restraints weight = 41456.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.073247 restraints weight = 30328.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.074211 restraints weight = 23782.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.074844 restraints weight = 19539.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.5757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10658  Z= 0.140
  Angle     :  0.740  14.459  14519  Z= 0.378
  Chirality :  0.048   0.263   1686
  Planarity :  0.004   0.040   1879
  Dihedral  :  6.346  33.350   1491
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.09 %
    Favored  : 84.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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 are not related in a simple way.
  whole: -3.37 (0.20), residues: 1385
  helix: -0.11 (0.32), residues: 245
  sheet: -2.31 (0.39), residues: 158
  loop : -3.04 (0.17), residues: 982

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  97 
 TYR   0.020   0.002   TYR E 984 
 PHE   0.022   0.002   PHE B  58 
 TRP   0.024   0.002   TRP A 183 
 HIS   0.005   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10658)
  covalent geometry    : angle       0.73964 (14519)
  hydrogen bonds       : bond        0.03269 (  223)
  hydrogen bonds       : angle       4.80906 (  627)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.425 
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: E  825 PHE cc_start: 0.6894 (m-10) cc_final: 0.6315 (m-10)
REVERT: K   92 MET cc_start: 0.4428 (pmm) cc_final: 0.3441 (pmm)
REVERT: K  483 LYS cc_start: 0.9030 (mptt) cc_final: 0.8362 (mttm)
REVERT: M  135 LEU cc_start: 0.8491 (pt) cc_final: 0.8178 (pt)
REVERT: M  139 ARG cc_start: 0.8982 (mmp-170) cc_final: 0.8307 (mmt180)
REVERT: M  160 GLN cc_start: 0.6516 (pt0) cc_final: 0.5393 (tp40)
REVERT: F  199 SER cc_start: 0.8896 (t) cc_final: 0.8668 (m)
REVERT: F  291 LYS cc_start: 0.7733 (pttp) cc_final: 0.6237 (mmmt)
REVERT: B   54 ASP cc_start: 0.8267 (p0) cc_final: 0.7389 (p0)
REVERT: B   83 ASP cc_start: 0.7882 (t0) cc_final: 0.7567 (t0)
REVERT: B  199 HIS cc_start: 0.7402 (t70) cc_final: 0.6769 (t70)
REVERT: B  261 GLN cc_start: 0.4966 (mt0) cc_final: 0.4688 (tt0)
REVERT: B  269 TRP cc_start: 0.8448 (m100) cc_final: 0.8185 (m-10)
REVERT: B  347 LYS cc_start: 0.8472 (mttt) cc_final: 0.8145 (mppt)
REVERT: B  354 ASP cc_start: 0.8924 (m-30) cc_final: 0.7694 (t0)
REVERT: A   42 ASN cc_start: 0.8905 (m-40) cc_final: 0.7906 (m110)
REVERT: A   54 HIS cc_start: 0.7272 (m90) cc_final: 0.6721 (m170)
REVERT: A  107 LYS cc_start: 0.9199 (mtpt) cc_final: 0.8469 (mtpt)
REVERT: A  109 ASN cc_start: 0.9268 (m110) cc_final: 0.8785 (m-40)
REVERT: A  233 GLU cc_start: 0.8233 (tp30) cc_final: 0.7869 (tp30)
REVERT: A  241 CYS cc_start: 0.8144 (p) cc_final: 0.7438 (m)
REVERT: A  291 MET cc_start: 0.7967 (tpp) cc_final: 0.7166 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0870
  time to fit residues: 25.8613
Evaluate side-chains
  144 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 130 optimal weight:    0.0980
   chunk 136 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 120 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 84 optimal weight:    7.9990
   chunk 61 optimal weight:    0.7980
   chunk 138 optimal weight:    5.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
** E1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A 105 ASN
A 127 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.079273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.067277 restraints weight = 62155.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.069129 restraints weight = 40695.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.070452 restraints weight = 29414.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.071411 restraints weight = 22860.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.072117 restraints weight = 18743.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.5789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10658  Z= 0.186
  Angle     :  0.781  12.981  14519  Z= 0.404
  Chirality :  0.049   0.262   1686
  Planarity :  0.004   0.039   1879
  Dihedral  :  6.624  34.559   1491
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 20.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 16.17 %
    Favored  : 83.75 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.77 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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 are not related in a simple way.
  whole: -3.39 (0.20), residues: 1385
  helix: -0.08 (0.32), residues: 238
  sheet: -2.30 (0.40), residues: 147
  loop : -3.05 (0.17), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K  97 
 TYR   0.021   0.002   TYR A 260 
 PHE   0.022   0.002   PHE B  58 
 TRP   0.023   0.002   TRP B 320 
 HIS   0.005   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (10658)
  covalent geometry    : angle       0.78118 (14519)
  hydrogen bonds       : bond        0.03597 (  223)
  hydrogen bonds       : angle       5.06839 (  627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2094.86 seconds
wall clock time: 37 minutes 1.08 seconds (2221.08 seconds total)