Starting phenix.real_space_refine
on Wed Sep 25 14:36:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/09_2024/6bx3_7303.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/09_2024/6bx3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/09_2024/6bx3_7303.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/09_2024/6bx3_7303.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/09_2024/6bx3_7303.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/09_2024/6bx3_7303.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.030
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4}
          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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5}
          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: {'GLU:plan': 2, 'ARG:plan': 1}
          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: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9}
          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: {'GLN:plan1': 5, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 5}
          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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 76
  Time building chain proxies: 6.25, per 1000 atoms: 0.60
  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: 2.64
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 1.01
  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: 2.95

  Time building geometry restraints manager: 3.06 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:             1.210
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.810
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.430
-------------------------------------------------------------------------------
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= 0.499
  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 : 24.88
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.033   0.004   TRP K 135 
 HIS   0.015   0.003   HIS A 286 
 PHE   0.030   0.004   PHE F 283 
 TYR   0.031   0.004   TYR K 202 
 ARG   0.009   0.001   ARG E 841 

*********************** 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 fitting.
    rotamer outliers: 10
    poor density    : 283
  time to evaluate  : 1.147 
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: symmetry clash
REVERT: E  819 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9165 (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: 0.8650 (tpp)
REVERT: E  998 ASP cc_start: 0.7816 (m-30) cc_final: 0.6241 (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: 0.8996 (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: 0.7381 (p0)
REVERT: B   59 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.8394 (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: 0.8009 (pp30)
REVERT: B  319 ASN cc_start: 0.9046 (t0) cc_final: 0.8768 (t0)
REVERT: B  320 TRP cc_start: 0.8524 (m100) cc_final: 0.8259 (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: 0.8848 (t0)
REVERT: A  149 ASN cc_start: 0.9139 (m-40) cc_final: 0.8871 (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: 0.7594 (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: 0.2427
  time to fit residues: 96.6924
Evaluate side-chains
  176 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 172
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0770
   chunk 58 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 108 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 126 optimal weight:   10.0000
   overall best weight:    2.3942

-------------------------------------------------------------------------------
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 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
B 336 ASN
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 HIS
A 294 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10658  Z= 0.269
  Angle     :  0.870  15.201  14519  Z= 0.457
  Chirality :  0.052   0.397   1686
  Planarity :  0.005   0.047   1879
  Dihedral  :  8.808  48.084   1491
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.82 %
    Favored  : 83.18 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  4.54 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.67 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.37 (0.19), residues: 1385
  helix: -1.89 (0.28), residues: 253
  sheet: -3.05 (0.34), residues: 182
  loop : -3.40 (0.17), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP K 135 
 HIS   0.010   0.002   HIS A  95 
 PHE   0.023   0.002   PHE B 355 
 TYR   0.024   0.002   TYR M 156 
 ARG   0.004   0.001   ARG A 225 

*********************** 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
  242 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 238
  time to evaluate  : 1.151 
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  934 ASN cc_start: 0.9177 (t0) cc_final: 0.8883 (p0)
REVERT: E  950 TRP cc_start: 0.7592 (m100) cc_final: 0.7315 (m100)
REVERT: E  975 PRO cc_start: 0.8071 (Cg_exo) cc_final: 0.7814 (Cg_endo)
REVERT: E  979 MET cc_start: 0.8994 (tpt) cc_final: 0.8698 (tpp)
REVERT: E  998 ASP cc_start: 0.7603 (m-30) cc_final: 0.6790 (m-30)
REVERT: K  135 TRP cc_start: 0.8696 (t60) cc_final: 0.8337 (t60)
REVERT: K  194 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8344 (tp30)
REVERT: K  199 PHE cc_start: 0.9320 (t80) cc_final: 0.9022 (t80)
REVERT: K  439 THR cc_start: 0.5787 (OUTLIER) cc_final: 0.5565 (p)
REVERT: K  483 LYS cc_start: 0.9293 (mptt) cc_final: 0.8570 (mtpt)
REVERT: M  139 ARG cc_start: 0.8918 (mmp-170) cc_final: 0.8139 (mtt180)
REVERT: M  156 TYR cc_start: 0.8597 (t80) cc_final: 0.8396 (t80)
REVERT: F  120 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8262 (mm-30)
REVERT: F  266 CYS cc_start: 0.8155 (p) cc_final: 0.7901 (p)
REVERT: F  291 LYS cc_start: 0.7807 (pttp) cc_final: 0.6494 (mmmt)
REVERT: B   83 ASP cc_start: 0.8240 (t0) cc_final: 0.7856 (t0)
REVERT: B  106 LYS cc_start: 0.8572 (tttp) cc_final: 0.8270 (mtmm)
REVERT: B  199 HIS cc_start: 0.6555 (m90) cc_final: 0.6282 (t70)
REVERT: B  319 ASN cc_start: 0.9116 (t0) cc_final: 0.8903 (t0)
REVERT: B  320 TRP cc_start: 0.8413 (m100) cc_final: 0.8070 (m100)
REVERT: B  354 ASP cc_start: 0.8912 (m-30) cc_final: 0.8081 (t0)
REVERT: A   26 GLN cc_start: 0.9041 (mp10) cc_final: 0.8770 (mp10)
REVERT: A  127 ASN cc_start: 0.9360 (t0) cc_final: 0.9157 (t0)
REVERT: A  149 ASN cc_start: 0.9165 (m-40) cc_final: 0.8752 (m-40)
REVERT: A  154 LEU cc_start: 0.8610 (tp) cc_final: 0.8154 (tp)
REVERT: A  194 GLN cc_start: 0.9013 (mt0) cc_final: 0.8716 (mt0)
REVERT: A  195 VAL cc_start: 0.8512 (m) cc_final: 0.7665 (p)
REVERT: A  199 GLU cc_start: 0.8843 (pm20) cc_final: 0.8378 (pm20)
REVERT: A  233 GLU cc_start: 0.7715 (tp30) cc_final: 0.7367 (tp30)
REVERT: A  291 MET cc_start: 0.8282 (tpp) cc_final: 0.7286 (mmp)
  outliers start: 4
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2159
  time to fit residues: 72.9327
Evaluate side-chains
  166 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 105 optimal weight:   20.0000
   chunk 85 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 126 optimal weight:    8.9990
   chunk 136 optimal weight:    9.9990
   chunk 112 optimal weight:    9.9990
   chunk 125 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 145 GLN
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 ASN
A  48 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  10658  Z= 0.430
  Angle     :  0.946  14.821  14519  Z= 0.497
  Chirality :  0.055   0.360   1686
  Planarity :  0.006   0.054   1879
  Dihedral  :  8.693  46.342   1491
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 26.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.71 %
    Favored  : 80.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.19), residues: 1385
  helix: -1.60 (0.28), residues: 246
  sheet: -3.04 (0.36), residues: 153
  loop : -3.48 (0.17), residues: 986

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP K 135 
 HIS   0.011   0.003   HIS A  95 
 PHE   0.021   0.003   PHE B 198 
 TYR   0.025   0.003   TYR B 364 
 ARG   0.008   0.001   ARG E 841 

*********************** 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
  192 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.362 
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: E  934 ASN cc_start: 0.9146 (t0) cc_final: 0.8842 (p0)
REVERT: E  998 ASP cc_start: 0.7673 (m-30) cc_final: 0.6875 (m-30)
REVERT: K  194 GLU cc_start: 0.8722 (mm-30) cc_final: 0.7901 (tm-30)
REVERT: K  483 LYS cc_start: 0.9161 (mptt) cc_final: 0.8532 (mttm)
REVERT: M  139 ARG cc_start: 0.8956 (mmp-170) cc_final: 0.8249 (mtt180)
REVERT: M  156 TYR cc_start: 0.8887 (t80) cc_final: 0.8686 (t80)
REVERT: F  120 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8284 (mp0)
REVERT: F  266 CYS cc_start: 0.8778 (p) cc_final: 0.8487 (p)
REVERT: F  291 LYS cc_start: 0.8017 (pttp) cc_final: 0.7627 (pttm)
REVERT: F  322 LEU cc_start: 0.9432 (mm) cc_final: 0.9119 (mm)
REVERT: B  106 LYS cc_start: 0.8715 (tttp) cc_final: 0.8363 (mtmm)
REVERT: B  319 ASN cc_start: 0.9257 (t0) cc_final: 0.8943 (t0)
REVERT: B  354 ASP cc_start: 0.9080 (m-30) cc_final: 0.8117 (t0)
REVERT: A  109 ASN cc_start: 0.9432 (m110) cc_final: 0.8990 (m-40)
REVERT: A  127 ASN cc_start: 0.9382 (t0) cc_final: 0.9169 (t0)
REVERT: A  145 ASP cc_start: 0.7870 (m-30) cc_final: 0.7608 (m-30)
REVERT: A  149 ASN cc_start: 0.9311 (m-40) cc_final: 0.8816 (m-40)
REVERT: A  154 LEU cc_start: 0.8658 (tp) cc_final: 0.8253 (tp)
REVERT: A  183 TRP cc_start: 0.7592 (p-90) cc_final: 0.7159 (p-90)
REVERT: A  185 ARG cc_start: 0.8660 (mmt90) cc_final: 0.8445 (mtp85)
REVERT: A  195 VAL cc_start: 0.8653 (m) cc_final: 0.7759 (p)
REVERT: A  199 GLU cc_start: 0.9018 (pm20) cc_final: 0.8764 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2162
  time to fit residues: 59.3967
Evaluate side-chains
  145 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0570
   chunk 60 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 126 optimal weight:    3.9990
   chunk 134 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 120 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0670
   overall best weight:    0.5236

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

Flipped N/Q/H residues before XYZ refinement:
E 932 GLN
** 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 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 330 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10658  Z= 0.220
  Angle     :  0.789  10.506  14519  Z= 0.408
  Chirality :  0.049   0.208   1686
  Planarity :  0.004   0.052   1879
  Dihedral  :  7.701  42.151   1491
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.68 %
    Favored  : 83.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.86 (0.20), residues: 1385
  helix: -0.79 (0.32), residues: 241
  sheet: -2.79 (0.38), residues: 152
  loop : -3.25 (0.17), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP E 950 
 HIS   0.006   0.001   HIS B  71 
 PHE   0.020   0.002   PHE B  58 
 TYR   0.017   0.002   TYR A 284 
 ARG   0.011   0.001   ARG B  59 

*********************** 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
  210 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.279 
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: E  934 ASN cc_start: 0.8999 (t0) cc_final: 0.8753 (p0)
REVERT: E  998 ASP cc_start: 0.7333 (m-30) cc_final: 0.6544 (m-30)
REVERT: K  483 LYS cc_start: 0.9101 (mptt) cc_final: 0.8449 (mttm)
REVERT: M  139 ARG cc_start: 0.8932 (mmp-170) cc_final: 0.8270 (mtt180)
REVERT: F  291 LYS cc_start: 0.7743 (pttp) cc_final: 0.7372 (pttm)
REVERT: B   54 ASP cc_start: 0.8284 (p0) cc_final: 0.7394 (p0)
REVERT: B  319 ASN cc_start: 0.9145 (t0) cc_final: 0.8890 (t0)
REVERT: B  354 ASP cc_start: 0.9010 (m-30) cc_final: 0.8090 (t0)
REVERT: A  107 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8784 (mtpt)
REVERT: A  109 ASN cc_start: 0.9354 (m110) cc_final: 0.8852 (m110)
REVERT: A  145 ASP cc_start: 0.7595 (m-30) cc_final: 0.7371 (m-30)
REVERT: A  149 ASN cc_start: 0.9245 (m-40) cc_final: 0.8695 (m-40)
REVERT: A  155 SER cc_start: 0.7308 (p) cc_final: 0.7006 (p)
REVERT: A  185 ARG cc_start: 0.8488 (mmt90) cc_final: 0.8175 (mtp85)
REVERT: A  195 VAL cc_start: 0.8484 (m) cc_final: 0.7748 (p)
REVERT: A  199 GLU cc_start: 0.8458 (pm20) cc_final: 0.8094 (pm20)
REVERT: A  238 HIS cc_start: 0.7738 (p-80) cc_final: 0.7299 (p-80)
REVERT: A  291 MET cc_start: 0.8322 (tpp) cc_final: 0.7114 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.1973
  time to fit residues: 60.0210
Evaluate side-chains
  153 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 76 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 55 optimal weight:    0.1980
   chunk 114 optimal weight:    5.9990
   chunk 92 optimal weight:    0.1980
   chunk 0 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9980
   chunk 120 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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**
K 225 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 330 ASN
A 127 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10658  Z= 0.205
  Angle     :  0.750  10.438  14519  Z= 0.388
  Chirality :  0.048   0.224   1686
  Planarity :  0.004   0.049   1879
  Dihedral  :  7.245  40.653   1491
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.97 %
    Favored  : 83.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.70 (0.20), residues: 1385
  helix: -0.67 (0.31), residues: 249
  sheet: -2.58 (0.38), residues: 168
  loop : -3.17 (0.18), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 183 
 HIS   0.010   0.001   HIS B  71 
 PHE   0.026   0.002   PHE A  58 
 TYR   0.023   0.002   TYR B  53 
 ARG   0.003   0.000   ARG B  85 

*********************** 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
  200 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.154 
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: E  934 ASN cc_start: 0.8926 (t0) cc_final: 0.8674 (p0)
REVERT: K  117 TYR cc_start: 0.5582 (m-10) cc_final: 0.5304 (m-80)
REVERT: K  483 LYS cc_start: 0.9096 (mptt) cc_final: 0.8437 (mttm)
REVERT: M  135 LEU cc_start: 0.8633 (pp) cc_final: 0.8404 (pp)
REVERT: M  139 ARG cc_start: 0.8939 (mmp-170) cc_final: 0.8258 (mtt180)
REVERT: M  156 TYR cc_start: 0.8585 (t80) cc_final: 0.8137 (t80)
REVERT: M  160 GLN cc_start: 0.7278 (tt0) cc_final: 0.6502 (tp40)
REVERT: F  120 GLU cc_start: 0.8481 (mp0) cc_final: 0.8132 (mp0)
REVERT: F  199 SER cc_start: 0.9133 (t) cc_final: 0.8896 (m)
REVERT: F  224 MET cc_start: 0.8574 (mmm) cc_final: 0.8312 (mmm)
REVERT: F  291 LYS cc_start: 0.7673 (pttp) cc_final: 0.7289 (pttm)
REVERT: B   54 ASP cc_start: 0.8186 (p0) cc_final: 0.7052 (p0)
REVERT: B  199 HIS cc_start: 0.6854 (t70) cc_final: 0.6436 (t70)
REVERT: B  354 ASP cc_start: 0.9043 (m-30) cc_final: 0.8069 (t0)
REVERT: A   26 GLN cc_start: 0.9007 (mp10) cc_final: 0.8779 (mp10)
REVERT: A   54 HIS cc_start: 0.7010 (m90) cc_final: 0.6653 (m-70)
REVERT: A  107 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8762 (mtpt)
REVERT: A  109 ASN cc_start: 0.9353 (m110) cc_final: 0.8852 (m110)
REVERT: A  142 VAL cc_start: 0.9289 (p) cc_final: 0.8936 (m)
REVERT: A  149 ASN cc_start: 0.9229 (m-40) cc_final: 0.8705 (m-40)
REVERT: A  155 SER cc_start: 0.7248 (p) cc_final: 0.6962 (p)
REVERT: A  185 ARG cc_start: 0.8534 (mmt90) cc_final: 0.8286 (mtp85)
REVERT: A  194 GLN cc_start: 0.8964 (mt0) cc_final: 0.8310 (mt0)
REVERT: A  195 VAL cc_start: 0.8530 (m) cc_final: 0.7823 (p)
REVERT: A  199 GLU cc_start: 0.8566 (pm20) cc_final: 0.8311 (pm20)
REVERT: A  238 HIS cc_start: 0.7694 (p-80) cc_final: 0.7289 (p-80)
REVERT: A  291 MET cc_start: 0.8395 (tpp) cc_final: 0.6977 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.2016
  time to fit residues: 58.1836
Evaluate side-chains
  149 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 134 optimal weight:    2.9990
   chunk 111 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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**
E1000 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
A 127 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.4880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10658  Z= 0.238
  Angle     :  0.752  10.874  14519  Z= 0.389
  Chirality :  0.048   0.232   1686
  Planarity :  0.005   0.077   1879
  Dihedral  :  7.137  39.859   1491
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 18.53
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 17.11 %
    Favored  : 82.82 %
  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 : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.21), residues: 1385
  helix: -0.50 (0.32), residues: 251
  sheet: -2.59 (0.38), residues: 170
  loop : -3.17 (0.18), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP K 135 
 HIS   0.012   0.002   HIS B  71 
 PHE   0.022   0.002   PHE B  58 
 TYR   0.020   0.002   TYR B  53 
 ARG   0.011   0.001   ARG K 188 

*********************** 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
  192 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.217 
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  825 PHE cc_start: 0.7119 (m-10) cc_final: 0.6791 (m-10)
REVERT: K  117 TYR cc_start: 0.5693 (m-10) cc_final: 0.5348 (m-80)
REVERT: K  483 LYS cc_start: 0.9098 (mptt) cc_final: 0.8465 (mttm)
REVERT: M  135 LEU cc_start: 0.8866 (pp) cc_final: 0.8389 (pp)
REVERT: M  139 ARG cc_start: 0.8968 (mmp-170) cc_final: 0.8225 (mtt180)
REVERT: M  156 TYR cc_start: 0.8666 (t80) cc_final: 0.8238 (t80)
REVERT: M  160 GLN cc_start: 0.7357 (tt0) cc_final: 0.6497 (tp40)
REVERT: F  120 GLU cc_start: 0.8535 (mp0) cc_final: 0.8096 (mp0)
REVERT: F  199 SER cc_start: 0.9125 (t) cc_final: 0.8884 (m)
REVERT: F  291 LYS cc_start: 0.7633 (pttp) cc_final: 0.7249 (pttm)
REVERT: B   54 ASP cc_start: 0.8134 (p0) cc_final: 0.6971 (p0)
REVERT: B  354 ASP cc_start: 0.9095 (m-30) cc_final: 0.8173 (t0)
REVERT: A   54 HIS cc_start: 0.7252 (m90) cc_final: 0.6657 (m-70)
REVERT: A   88 LEU cc_start: 0.6907 (tt) cc_final: 0.6688 (tt)
REVERT: A  107 LYS cc_start: 0.9313 (mtpt) cc_final: 0.8734 (mtpt)
REVERT: A  109 ASN cc_start: 0.9387 (m110) cc_final: 0.8862 (m110)
REVERT: A  112 PHE cc_start: 0.6709 (m-80) cc_final: 0.6507 (m-10)
REVERT: A  149 ASN cc_start: 0.9283 (m-40) cc_final: 0.8765 (m-40)
REVERT: A  155 SER cc_start: 0.7453 (p) cc_final: 0.7106 (p)
REVERT: A  173 CYS cc_start: 0.8992 (m) cc_final: 0.8741 (m)
REVERT: A  185 ARG cc_start: 0.8542 (mmt90) cc_final: 0.8204 (mtt90)
REVERT: A  194 GLN cc_start: 0.9030 (mt0) cc_final: 0.8778 (mt0)
REVERT: A  195 VAL cc_start: 0.8573 (m) cc_final: 0.7928 (p)
REVERT: A  291 MET cc_start: 0.8445 (tpp) cc_final: 0.7105 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2153
  time to fit residues: 58.6325
Evaluate side-chains
  146 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 129 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 98 optimal weight:    8.9990
   chunk 113 optimal weight:    7.9990
   chunk 75 optimal weight:    0.4980
   chunk 133 optimal weight:    9.9990
   chunk 83 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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**
K 476 ASN
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** 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
A 127 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.5136

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= 0.196
  Angle     :  0.748  11.543  14519  Z= 0.383
  Chirality :  0.048   0.244   1686
  Planarity :  0.004   0.049   1879
  Dihedral  :  6.806  38.032   1491
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.23 %
    Favored  : 84.69 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.22 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.21), residues: 1385
  helix: -0.24 (0.33), residues: 240
  sheet: -2.15 (0.42), residues: 141
  loop : -3.15 (0.18), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 183 
 HIS   0.010   0.001   HIS B  71 
 PHE   0.021   0.002   PHE B  58 
 TYR   0.014   0.002   TYR A 284 
 ARG   0.004   0.000   ARG E 973 

*********************** 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
  206 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 1.235 
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  815 ASP cc_start: 0.9052 (t0) cc_final: 0.8496 (t0)
REVERT: E  819 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8901 (mm-30)
REVERT: E  978 GLU cc_start: 0.9542 (tm-30) cc_final: 0.9279 (tm-30)
REVERT: E  979 MET cc_start: 0.8895 (tpt) cc_final: 0.8675 (tpp)
REVERT: K  117 TYR cc_start: 0.5412 (m-10) cc_final: 0.5112 (m-10)
REVERT: K  199 PHE cc_start: 0.8633 (t80) cc_final: 0.8308 (t80)
REVERT: M  135 LEU cc_start: 0.8841 (pp) cc_final: 0.8447 (pp)
REVERT: M  139 ARG cc_start: 0.8953 (mmp-170) cc_final: 0.8322 (mmt180)
REVERT: M  156 TYR cc_start: 0.8632 (t80) cc_final: 0.8243 (t80)
REVERT: M  160 GLN cc_start: 0.7332 (tt0) cc_final: 0.6521 (tp40)
REVERT: F  120 GLU cc_start: 0.8490 (mp0) cc_final: 0.8043 (mp0)
REVERT: F  199 SER cc_start: 0.9023 (t) cc_final: 0.8796 (m)
REVERT: F  291 LYS cc_start: 0.7616 (pttp) cc_final: 0.7223 (pttm)
REVERT: B   54 ASP cc_start: 0.8148 (p0) cc_final: 0.7233 (p0)
REVERT: B   83 ASP cc_start: 0.8170 (t0) cc_final: 0.7752 (t70)
REVERT: B  148 ASP cc_start: 0.7495 (m-30) cc_final: 0.7190 (m-30)
REVERT: B  325 MET cc_start: 0.8648 (mmp) cc_final: 0.7518 (ppp)
REVERT: B  354 ASP cc_start: 0.9086 (m-30) cc_final: 0.8152 (t0)
REVERT: A   42 ASN cc_start: 0.9045 (m-40) cc_final: 0.7949 (m-40)
REVERT: A   54 HIS cc_start: 0.7200 (m90) cc_final: 0.6583 (m170)
REVERT: A   68 GLN cc_start: 0.8481 (tt0) cc_final: 0.8184 (tm-30)
REVERT: A  107 LYS cc_start: 0.9283 (mtpt) cc_final: 0.8655 (mtpt)
REVERT: A  109 ASN cc_start: 0.9318 (m110) cc_final: 0.8821 (m110)
REVERT: A  142 VAL cc_start: 0.9250 (p) cc_final: 0.8908 (m)
REVERT: A  149 ASN cc_start: 0.9290 (m-40) cc_final: 0.8896 (m-40)
REVERT: A  155 SER cc_start: 0.7327 (p) cc_final: 0.7055 (p)
REVERT: A  185 ARG cc_start: 0.8469 (mmt90) cc_final: 0.8134 (mtt90)
REVERT: A  194 GLN cc_start: 0.9028 (mt0) cc_final: 0.8743 (mt0)
REVERT: A  195 VAL cc_start: 0.8488 (m) cc_final: 0.7831 (p)
REVERT: A  241 CYS cc_start: 0.8373 (p) cc_final: 0.7486 (m)
REVERT: A  291 MET cc_start: 0.8407 (tpp) cc_final: 0.6937 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 205
  average time/residue: 0.2021
  time to fit residues: 60.0544
Evaluate side-chains
  149 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 26 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 105 optimal weight:    9.9990
   chunk 121 optimal weight:    0.8980
   overall best weight:    2.6786

-------------------------------------------------------------------------------
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 444 ASN
** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 144 GLN
** 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 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 ASN
A 127 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.5302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10658  Z= 0.257
  Angle     :  0.769  10.871  14519  Z= 0.399
  Chirality :  0.049   0.247   1686
  Planarity :  0.004   0.049   1879
  Dihedral  :  6.920  38.635   1491
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 20.13
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 17.76 %
    Favored  : 82.17 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.35 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.21), residues: 1385
  helix: -0.21 (0.32), residues: 246
  sheet: -2.56 (0.39), residues: 156
  loop : -3.15 (0.18), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP K 135 
 HIS   0.013   0.001   HIS B  71 
 PHE   0.025   0.002   PHE B  58 
 TYR   0.019   0.002   TYR F 344 
 ARG   0.006   0.001   ARG B 228 

*********************** 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
  191 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 189
  time to evaluate  : 1.223 
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: 0.9010 (t0) cc_final: 0.8406 (t0)
REVERT: E  819 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8911 (mm-30)
REVERT: K  117 TYR cc_start: 0.5672 (m-10) cc_final: 0.5292 (m-10)
REVERT: K  444 ASN cc_start: 0.6756 (OUTLIER) cc_final: 0.5662 (p0)
REVERT: K  483 LYS cc_start: 0.9037 (mptt) cc_final: 0.8407 (mttm)
REVERT: M  139 ARG cc_start: 0.8935 (mmp-170) cc_final: 0.8556 (mmt180)
REVERT: M  156 TYR cc_start: 0.8698 (t80) cc_final: 0.8291 (t80)
REVERT: M  160 GLN cc_start: 0.7470 (tt0) cc_final: 0.6634 (tp40)
REVERT: F  199 SER cc_start: 0.9076 (t) cc_final: 0.8836 (m)
REVERT: F  269 TYR cc_start: 0.7916 (p90) cc_final: 0.7550 (p90)
REVERT: F  291 LYS cc_start: 0.7553 (pttp) cc_final: 0.6154 (mmmt)
REVERT: B   54 ASP cc_start: 0.8256 (p0) cc_final: 0.7236 (p0)
REVERT: B   83 ASP cc_start: 0.8222 (t0) cc_final: 0.7795 (t70)
REVERT: B  148 ASP cc_start: 0.7495 (m-30) cc_final: 0.7156 (m-30)
REVERT: B  325 MET cc_start: 0.8754 (mmp) cc_final: 0.7675 (ppp)
REVERT: B  354 ASP cc_start: 0.9140 (m-30) cc_final: 0.8168 (t0)
REVERT: A   54 HIS cc_start: 0.7299 (m90) cc_final: 0.6686 (m170)
REVERT: A   68 GLN cc_start: 0.8476 (tt0) cc_final: 0.8153 (tm-30)
REVERT: A  107 LYS cc_start: 0.9315 (mtpt) cc_final: 0.8692 (mtpt)
REVERT: A  109 ASN cc_start: 0.9351 (m110) cc_final: 0.8875 (m110)
REVERT: A  149 ASN cc_start: 0.9287 (m-40) cc_final: 0.8906 (m-40)
REVERT: A  185 ARG cc_start: 0.8517 (mmt90) cc_final: 0.8006 (mtt90)
REVERT: A  194 GLN cc_start: 0.9101 (mt0) cc_final: 0.8755 (mt0)
REVERT: A  195 VAL cc_start: 0.8573 (m) cc_final: 0.8353 (p)
REVERT: A  241 CYS cc_start: 0.8487 (p) cc_final: 0.7643 (m)
REVERT: A  291 MET cc_start: 0.8512 (tpp) cc_final: 0.7007 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2145
  time to fit residues: 58.8920
Evaluate side-chains
  147 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 117 optimal weight:    1.9990
   chunk 124 optimal weight:    8.9990
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    0.2980
   chunk 98 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 112 optimal weight:    0.5980
   chunk 118 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0770
   chunk 132 optimal weight:    0.6980
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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 133 HIS
N 144 GLN
** 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 127 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.5607

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= 0.189
  Angle     :  0.751  11.174  14519  Z= 0.383
  Chirality :  0.048   0.256   1686
  Planarity :  0.004   0.050   1879
  Dihedral  :  6.546  35.527   1491
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.80 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.06 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.43 (0.21), residues: 1385
  helix: -0.01 (0.33), residues: 241
  sheet: -2.37 (0.38), residues: 153
  loop : -3.11 (0.18), residues: 991

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 183 
 HIS   0.008   0.001   HIS B  71 
 PHE   0.026   0.002   PHE B  58 
 TYR   0.019   0.002   TYR A 260 
 ARG   0.004   0.000   ARG E 973 

*********************** 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
  203 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 202
  time to evaluate  : 1.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  815 ASP cc_start: 0.9034 (t0) cc_final: 0.8460 (t0)
REVERT: E  819 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8902 (mm-30)
REVERT: K  117 TYR cc_start: 0.5491 (m-10) cc_final: 0.5214 (m-10)
REVERT: K  483 LYS cc_start: 0.8987 (mptt) cc_final: 0.8318 (mttm)
REVERT: M  139 ARG cc_start: 0.8930 (mmp-170) cc_final: 0.8367 (mmt180)
REVERT: M  156 TYR cc_start: 0.8597 (t80) cc_final: 0.8271 (t80)
REVERT: M  160 GLN cc_start: 0.7464 (tt0) cc_final: 0.6658 (tp40)
REVERT: F  204 LYS cc_start: 0.8602 (tppt) cc_final: 0.8361 (pttm)
REVERT: F  216 TRP cc_start: 0.8805 (m-90) cc_final: 0.8522 (t-100)
REVERT: F  269 TYR cc_start: 0.7773 (p90) cc_final: 0.7460 (p90)
REVERT: F  291 LYS cc_start: 0.7641 (pttp) cc_final: 0.7254 (pttm)
REVERT: B   54 ASP cc_start: 0.8288 (p0) cc_final: 0.7233 (p0)
REVERT: B   83 ASP cc_start: 0.8013 (t0) cc_final: 0.7617 (t0)
REVERT: B  148 ASP cc_start: 0.7468 (m-30) cc_final: 0.7161 (m-30)
REVERT: B  199 HIS cc_start: 0.7172 (t70) cc_final: 0.6828 (t70)
REVERT: B  325 MET cc_start: 0.8662 (mmp) cc_final: 0.7208 (ppp)
REVERT: B  354 ASP cc_start: 0.9102 (m-30) cc_final: 0.8159 (t0)
REVERT: A   42 ASN cc_start: 0.8970 (m-40) cc_final: 0.7946 (m-40)
REVERT: A   54 HIS cc_start: 0.7207 (m90) cc_final: 0.6605 (m170)
REVERT: A   68 GLN cc_start: 0.8422 (tt0) cc_final: 0.8154 (tm-30)
REVERT: A  107 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8944 (mtpt)
REVERT: A  109 ASN cc_start: 0.9220 (m110) cc_final: 0.8948 (m110)
REVERT: A  142 VAL cc_start: 0.9318 (p) cc_final: 0.8942 (m)
REVERT: A  185 ARG cc_start: 0.8422 (mmt90) cc_final: 0.8169 (mtt90)
REVERT: A  194 GLN cc_start: 0.9013 (mt0) cc_final: 0.8711 (mt0)
REVERT: A  195 VAL cc_start: 0.8564 (m) cc_final: 0.8111 (p)
REVERT: A  241 CYS cc_start: 0.8305 (p) cc_final: 0.7381 (m)
REVERT: A  260 TYR cc_start: 0.5577 (t80) cc_final: 0.4937 (t80)
REVERT: A  266 TYR cc_start: 0.8155 (m-80) cc_final: 0.7941 (m-10)
REVERT: A  291 MET cc_start: 0.8324 (tpp) cc_final: 0.6882 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 202
  average time/residue: 0.2068
  time to fit residues: 60.4469
Evaluate side-chains
  147 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 80 optimal weight:    0.4980
   chunk 62 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 138 optimal weight:   40.0000
   chunk 127 optimal weight:    9.9990
   chunk 110 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 85 optimal weight:    0.4980
   chunk 67 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 117 optimal weight:    8.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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**
N 144 GLN
** 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: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.5761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10658  Z= 0.202
  Angle     :  0.744  11.588  14519  Z= 0.382
  Chirality :  0.048   0.320   1686
  Planarity :  0.004   0.049   1879
  Dihedral  :  6.470  35.948   1491
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.74 %
    Favored  : 84.19 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.97 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.21), residues: 1385
  helix:  0.15 (0.33), residues: 241
  sheet: -2.56 (0.38), residues: 161
  loop : -3.05 (0.18), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 320 
 HIS   0.011   0.001   HIS B  71 
 PHE   0.025   0.002   PHE B  58 
 TYR   0.024   0.002   TYR A 260 
 ARG   0.004   0.000   ARG B 228 

********************** 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
  204 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 1.157 
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  815 ASP cc_start: 0.9026 (t0) cc_final: 0.8463 (t0)
REVERT: E  819 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8896 (mm-30)
REVERT: E  825 PHE cc_start: 0.7265 (m-10) cc_final: 0.6791 (m-10)
REVERT: K  117 TYR cc_start: 0.5697 (m-10) cc_final: 0.5266 (m-10)
REVERT: K  483 LYS cc_start: 0.8959 (mptt) cc_final: 0.8326 (mttm)
REVERT: M  139 ARG cc_start: 0.9010 (mmp-170) cc_final: 0.8661 (mmt180)
REVERT: M  156 TYR cc_start: 0.8683 (t80) cc_final: 0.8327 (t80)
REVERT: M  160 GLN cc_start: 0.7516 (tt0) cc_final: 0.6726 (tp40)
REVERT: F  269 TYR cc_start: 0.7862 (p90) cc_final: 0.7524 (p90)
REVERT: F  291 LYS cc_start: 0.7557 (pttp) cc_final: 0.6108 (mmmt)
REVERT: B   54 ASP cc_start: 0.8294 (p0) cc_final: 0.7227 (p0)
REVERT: B   83 ASP cc_start: 0.8038 (t0) cc_final: 0.7604 (t0)
REVERT: B  148 ASP cc_start: 0.7473 (m-30) cc_final: 0.7172 (m-30)
REVERT: B  199 HIS cc_start: 0.7252 (t70) cc_final: 0.6869 (t70)
REVERT: B  229 LEU cc_start: 0.9607 (mt) cc_final: 0.9348 (mt)
REVERT: B  240 GLN cc_start: 0.8595 (tt0) cc_final: 0.7724 (tp40)
REVERT: B  261 GLN cc_start: 0.5044 (mt0) cc_final: 0.4278 (tt0)
REVERT: B  325 MET cc_start: 0.8755 (mmp) cc_final: 0.7438 (ppp)
REVERT: B  354 ASP cc_start: 0.9101 (m-30) cc_final: 0.8177 (t0)
REVERT: A   42 ASN cc_start: 0.9001 (m-40) cc_final: 0.7985 (m110)
REVERT: A   68 GLN cc_start: 0.8429 (tt0) cc_final: 0.8155 (tm-30)
REVERT: A  107 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8766 (mtpt)
REVERT: A  109 ASN cc_start: 0.9247 (m110) cc_final: 0.8821 (m-40)
REVERT: A  142 VAL cc_start: 0.9252 (p) cc_final: 0.8903 (m)
REVERT: A  185 ARG cc_start: 0.8513 (mmt90) cc_final: 0.8267 (mtt90)
REVERT: A  194 GLN cc_start: 0.9035 (mt0) cc_final: 0.8683 (mt0)
REVERT: A  241 CYS cc_start: 0.8318 (p) cc_final: 0.7361 (m)
REVERT: A  260 TYR cc_start: 0.5341 (t80) cc_final: 0.5015 (t80)
REVERT: A  266 TYR cc_start: 0.8192 (m-80) cc_final: 0.7924 (m-10)
REVERT: A  291 MET cc_start: 0.8311 (tpp) cc_final: 0.6933 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2103
  time to fit residues: 61.6885
Evaluate side-chains
  149 residues out of total 1264 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 101 optimal weight:    7.9990
   chunk 16 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 110 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   chunk 113 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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**
** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 160 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**
A 127 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.078978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.067273 restraints weight = 62007.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.069072 restraints weight = 40869.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.070351 restraints weight = 29789.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.5786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10658  Z= 0.289
  Angle     :  0.796  11.362  14519  Z= 0.415
  Chirality :  0.050   0.311   1686
  Planarity :  0.005   0.059   1879
  Dihedral  :  6.848  36.873   1491
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 20.98
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 17.98 %
    Favored  : 81.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.20), residues: 1385
  helix: -0.08 (0.31), residues: 246
  sheet: -2.69 (0.37), residues: 165
  loop : -3.11 (0.18), residues: 974

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP B 320 
 HIS   0.013   0.002   HIS B  71 
 PHE   0.025   0.002   PHE B  58 
 TYR   0.027   0.002   TYR A 260 
 ARG   0.005   0.001   ARG E 980 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2401.07 seconds
wall clock time: 43 minutes 34.86 seconds (2614.86 seconds total)