Starting phenix.real_space_refine
on Thu Jan 16 01:01:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y81_39029/01_2025/8y81_39029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y81_39029/01_2025/8y81_39029.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y81_39029/01_2025/8y81_39029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y81_39029/01_2025/8y81_39029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y81_39029/01_2025/8y81_39029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y81_39029/01_2025/8y81_39029.cif"
  }
  resolution = 2.89
  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=   0.058
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      40      5.16       5
     C    5713      2.51       5
     N    1483      2.21       5
     O    1679      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8915
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1729
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 4, 'TRANS': 207}
    Chain: "B"
      Number of atoms: 1227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 158, 1227
          Classifications: {'peptide': 158}
          Link IDs: {'PTRANS': 1, 'TRANS': 156}
    Chain: "C"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 301
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "E"
      Number of atoms: 2602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 320, 2602
          Classifications: {'peptide': 320}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 300}
    Chain: "F"
      Number of atoms: 2571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2571
          Classifications: {'peptide': 316}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 295}
    Chain: "G"
      Number of atoms: 274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 274
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "T"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.63, per 1000 atoms: 0.63
  Number of scatterers: 8915
  At special positions: 0
  Unit cell: (148.73, 101.65, 112.35, 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      40     16.00
     O    1679      8.00
     N    1483      7.00
     C    5713      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A  91 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 130 " - pdb=" SG  CYS A 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  25 " - pdb=" SG  CYS G  25 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 112 " - pdb=" SG  CYS F 200 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 125 " - pdb=" SG  CYS E 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 230 " - pdb=" SG  CYS E 289 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 334 " - pdb=" SG  CYS E 396 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 125 " - pdb=" SG  CYS F 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 230 " - pdb=" SG  CYS F 289 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 334 " - pdb=" SG  CYS F 396 " distance=2.04

  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
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG T   1 " - " NAG T   2 "
    NAG-ASN
      " NAG A 301 " - " ASN A 158 "
      " NAG A 302 " - " ASN A 167 "
      " NAG D   1 " - " ASN E 265 "
      " NAG E 502 " - " ASN E 240 "
      " NAG F 501 " - " ASN F 170 "
      " NAG H   1 " - " ASN F 265 "
      " NAG T   1 " - " ASN A  65 "
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 848.1 milliseconds
  

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 19 sheets defined
      29.0% alpha, 35.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 86
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 200 through 204
    Processing helix  chain 'A' and resid 205 through 213
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 4.272A  pdb=" N   THR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLN A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.027A  pdb=" N   ILE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN A 236 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 231 through 236'
    Processing helix  chain 'B' and resid 51 through 56
      removed outlier: 3.642A  pdb=" N   LYS B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 83
      removed outlier: 4.362A  pdb=" N   GLN B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 88
      removed outlier: 3.593A  pdb=" N   PHE B  88 " --> pdb=" O   THR B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 98
    Processing helix  chain 'B' and resid 99 through 122
      removed outlier: 3.662A  pdb=" N   LEU B 107 " --> pdb=" O   TRP B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 160
    Processing helix  chain 'B' and resid 168 through 205
      removed outlier: 3.778A  pdb=" N   LEU B 187 " --> pdb=" O   MET B 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 58
    Processing helix  chain 'E' and resid 173 through 178
    Processing helix  chain 'E' and resid 216 through 222
    Processing helix  chain 'E' and resid 277 through 284
      removed outlier: 3.580A  pdb=" N   TRP E 281 " --> pdb=" O   ASP E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 385 through 389
    Processing helix  chain 'F' and resid 173 through 178
    Processing helix  chain 'F' and resid 204 through 208
    Processing helix  chain 'F' and resid 216 through 222
    Processing helix  chain 'F' and resid 277 through 284
    Processing helix  chain 'F' and resid 385 through 389
    Processing helix  chain 'G' and resid 25 through 56
      removed outlier: 3.693A  pdb=" N   LEU G  32 " --> pdb=" O   LEU G  28 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU G  39 " --> pdb=" O   TYR G  35 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ILE G  48 " --> pdb=" O   CYS G  44 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN G  49 " --> pdb=" O   ARG G  45 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 6.538A  pdb=" N   ILE A  39 " --> pdb=" O   MET A 107 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TRP A  62 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115
    Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 121
      removed outlier: 5.987A  pdb=" N   SER A 171 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   LYS A 145 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   HIS A 173 " --> pdb=" O   TYR A 143 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   TYR A 143 " --> pdb=" O   HIS A 173 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   THR A 175 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   VAL A 141 " --> pdb=" O   THR A 175 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   VAL A 141 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   TYR A 152 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   TYR A 143 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 121
    Processing sheet with id=AA6, first strand: chain 'E' and resid 104 through 109
      removed outlier: 5.273A  pdb=" N   ALA E 163 " --> pdb=" O   GLY E 129 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   LEU E 162 " --> pdb=" O   GLU E 158 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   GLU E 158 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   SER E 164 " --> pdb=" O   ILE E 156 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 144 through 145
    Processing sheet with id=AA8, first strand: chain 'E' and resid 209 through 213
      removed outlier: 5.463A  pdb=" N   THR E 229 " --> pdb=" O   LEU E 274 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   LEU E 274 " --> pdb=" O   THR E 229 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   LEU E 231 " --> pdb=" O   SER E 272 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   SER E 272 " --> pdb=" O   LEU E 231 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   LEU E 233 " --> pdb=" O   ILE E 270 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ILE E 270 " --> pdb=" O   LEU E 233 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 242 through 246
    Processing sheet with id=AB1, first strand: chain 'E' and resid 315 through 319
      removed outlier: 3.815A  pdb=" N   THR E 333 " --> pdb=" O   PHE E 319 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   PHE E 375 " --> pdb=" O   ASN E 338 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 315 through 319
      removed outlier: 3.815A  pdb=" N   THR E 333 " --> pdb=" O   PHE E 319 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   PHE E 375 " --> pdb=" O   ASN E 338 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 353 through 354
    Processing sheet with id=AB4, first strand: chain 'F' and resid 104 through 109
      removed outlier: 4.765A  pdb=" N   ALA F 163 " --> pdb=" O   GLY F 129 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   TYR F 166 " --> pdb=" O   LEU F 155 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   LEU F 155 " --> pdb=" O   TYR F 166 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 135 through 141
    Processing sheet with id=AB6, first strand: chain 'F' and resid 209 through 213
      removed outlier: 3.732A  pdb=" N   ASP F 234 " --> pdb=" O   THR F 268 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   THR F 268 " --> pdb=" O   ASP F 234 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 242 through 246
    Processing sheet with id=AB8, first strand: chain 'F' and resid 315 through 319
      removed outlier: 3.672A  pdb=" N   THR F 333 " --> pdb=" O   PHE F 319 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   PHE F 375 " --> pdb=" O   ASN F 338 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 319
      removed outlier: 3.672A  pdb=" N   THR F 333 " --> pdb=" O   PHE F 319 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   PHE F 375 " --> pdb=" O   ASN F 338 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 345 through 348

    460 hydrogen bonds defined for protein.
    1227 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: 3.02

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2042
        1.33 -     1.45: 2026
        1.45 -     1.57: 5003
        1.57 -     1.70: 1
        1.70 -     1.82: 49
  Bond restraints: 9121
  Sorted by residual:
  bond pdb=" CAX Y01 B 601 "
       pdb=" OAH Y01 B 601 "
    ideal  model  delta    sigma   weight residual
    1.248  1.342 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" N   GLU A 199 "
       pdb=" CA  GLU A 199 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.15e-02 7.56e+03 7.63e+00
  bond pdb=" CB  PRO E 103 "
       pdb=" CG  PRO E 103 "
    ideal  model  delta    sigma   weight residual
    1.492  1.611 -0.119 5.00e-02 4.00e+02 5.67e+00
  bond pdb=" C1  NAG E 502 "
       pdb=" O5  NAG E 502 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.69e+00
  bond pdb=" C1  NAG A 302 "
       pdb=" O5  NAG A 302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.68e+00
  ... (remaining 9116 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 11953
        2.42 -     4.85: 367
        4.85 -     7.27: 50
        7.27 -     9.70: 10
        9.70 -    12.12: 3
  Bond angle restraints: 12383
  Sorted by residual:
  angle pdb=" CA  PRO E 103 "
        pdb=" N   PRO E 103 "
        pdb=" CD  PRO E 103 "
      ideal   model   delta    sigma   weight residual
     112.00  104.98    7.02 1.40e+00 5.10e-01 2.52e+01
  angle pdb=" C   TYR F 368 "
        pdb=" N   ASN F 369 "
        pdb=" CA  ASN F 369 "
      ideal   model   delta    sigma   weight residual
     121.54  130.69   -9.15 1.91e+00 2.74e-01 2.29e+01
  angle pdb=" C   GLN E 390 "
        pdb=" N   THR E 391 "
        pdb=" CA  THR E 391 "
      ideal   model   delta    sigma   weight residual
     122.46  128.97   -6.51 1.41e+00 5.03e-01 2.13e+01
  angle pdb=" C   VAL B 127 "
        pdb=" N   ARG B 128 "
        pdb=" CA  ARG B 128 "
      ideal   model   delta    sigma   weight residual
     121.54  130.35   -8.81 1.91e+00 2.74e-01 2.13e+01
  angle pdb=" C   TYR E 368 "
        pdb=" N   ASN E 369 "
        pdb=" CA  ASN E 369 "
      ideal   model   delta    sigma   weight residual
     125.02  132.02   -7.00 1.76e+00 3.23e-01 1.58e+01
  ... (remaining 12378 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.62: 5267
       21.62 -    43.24: 360
       43.24 -    64.85: 51
       64.85 -    86.47: 28
       86.47 -   108.09: 10
  Dihedral angle restraints: 5716
    sinusoidal: 2532
      harmonic: 3184
  Sorted by residual:
  dihedral pdb=" CA  ASP A  33 "
           pdb=" C   ASP A  33 "
           pdb=" N   PRO A  34 "
           pdb=" CA  PRO A  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   99.19   80.81     0      5.00e+00 4.00e-02 2.61e+02
  dihedral pdb=" CA  ILE A 198 "
           pdb=" C   ILE A 198 "
           pdb=" N   GLU A 199 "
           pdb=" CA  GLU A 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.60   39.40     0      5.00e+00 4.00e-02 6.21e+01
  dihedral pdb=" CA  ASN A 179 "
           pdb=" C   ASN A 179 "
           pdb=" N   LYS A 180 "
           pdb=" CA  LYS A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.34   36.66     0      5.00e+00 4.00e-02 5.38e+01
  ... (remaining 5713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1161
       0.074 -    0.148: 254
       0.148 -    0.223: 26
       0.223 -    0.297: 9
       0.297 -    0.371: 2
  Chirality restraints: 1452
  Sorted by residual:
  chirality pdb=" CB  ILE F 413 "
            pdb=" CA  ILE F 413 "
            pdb=" CG1 ILE F 413 "
            pdb=" CG2 ILE F 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.44e+00
  chirality pdb=" CBH Y01 B 601 "
            pdb=" CAT Y01 B 601 "
            pdb=" CAZ Y01 B 601 "
            pdb=" CBF Y01 B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.52   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CBG Y01 B 601 "
            pdb=" CAQ Y01 B 601 "
            pdb=" CBD Y01 B 601 "
            pdb=" CBI Y01 B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.62    0.29 2.00e-01 2.50e+01 2.11e+00
  ... (remaining 1449 not shown)

  Planarity restraints: 1526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 198 "   -0.027 2.00e-02 2.50e+03   5.31e-02 2.82e+01
        pdb=" C   ILE A 198 "    0.092 2.00e-02 2.50e+03
        pdb=" O   ILE A 198 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   GLU A 199 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 154 "    0.022 2.00e-02 2.50e+03   2.50e-02 1.25e+01
        pdb=" CG  TYR A 154 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 154 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 154 "    0.028 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 154 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 154 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 154 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 154 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  33 "    0.047 5.00e-02 4.00e+02   7.29e-02 8.51e+00
        pdb=" N   PRO A  34 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO A  34 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A  34 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1523 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2080
        2.80 -     3.32: 7809
        3.32 -     3.85: 15182
        3.85 -     4.37: 17784
        4.37 -     4.90: 30761
  Nonbonded interactions: 73616
  Sorted by model distance:
  nonbonded pdb=" O   VAL B  78 "
            pdb=" OG1 THR B  82 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   THR B 174 "
            pdb=" OG1 THR B 178 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   ASP E 142 "
            pdb=" O6  NAG D   1 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OD2 ASP E 143 "
            pdb=" ND1 HIS E 263 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OH  TYR C  35 "
            pdb=" OG1 THR G  40 "
     model   vdw
     2.287 3.040
  ... (remaining 73611 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 'C' and resid 24 through 57)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'E' and (resid 101 through 416 or resid 502))
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.720
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.640
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  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:11.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
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   0.119   9121  Z= 0.463
  Angle     :  0.997  12.122  12383  Z= 0.525
  Chirality :  0.063   0.371   1452
  Planarity :  0.007   0.073   1519
  Dihedral  : 16.035 108.091   3613
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.85 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.61 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.29 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.24), residues: 1065
  helix: -1.51 (0.25), residues: 279
  sheet: -0.11 (0.29), residues: 321
  loop : -0.83 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 103 
 HIS   0.011   0.002   HIS F 295 
 PHE   0.036   0.003   PHE E 117 
 TYR   0.059   0.003   TYR A 154 
 ARG   0.004   0.000   ARG E 144 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 1.0864
  time to fit residues: 147.6446
Evaluate side-chains
  83 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 44 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 108 GLN
B 134 ASN
B 151 ASN
** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 HIS
E 153 ASN
E 174 GLN
** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 264 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.171626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.133654 restraints weight = 10334.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.15
r_work: 0.3272 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9121  Z= 0.255
  Angle     :  0.632  10.306  12383  Z= 0.330
  Chirality :  0.046   0.153   1452
  Planarity :  0.005   0.062   1519
  Dihedral  : 11.182  75.612   1504
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  8.27 %
    Favored  : 90.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.24), residues: 1065
  helix: -0.35 (0.27), residues: 282
  sheet: -0.00 (0.29), residues: 324
  loop : -0.52 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 222 
 HIS   0.006   0.001   HIS F 295 
 PHE   0.019   0.002   PHE E 117 
 TYR   0.017   0.001   TYR G  35 
 ARG   0.005   0.001   ARG E 330 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8641 (ttp-170) cc_final: 0.8313 (ttp-170)
REVERT: E  141 MET cc_start: 0.8361 (ttt) cc_final: 0.8032 (ttp)
REVERT: E  372 ASN cc_start: 0.6349 (t0) cc_final: 0.6126 (t0)
  outliers start: 16
  outliers final: 7
  residues processed: 99
  average time/residue: 1.0181
  time to fit residues: 109.6951
Evaluate side-chains
  90 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLN
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain E residue  229 THR
Chi-restraints excluded: chain E residue  244 THR
Chi-restraints excluded: chain F residue  343 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 76 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0050
   chunk 96 optimal weight:    0.0980
   chunk 43 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
B 134 ASN
** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 HIS
E 153 ASN
E 223 ASN
F 118 HIS
F 264 HIS
F 373 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.172564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.133641 restraints weight = 10421.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.18
r_work: 0.3295 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9121  Z= 0.184
  Angle     :  0.570  10.516  12383  Z= 0.297
  Chirality :  0.045   0.150   1452
  Planarity :  0.004   0.060   1519
  Dihedral  :  9.322  73.227   1504
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.70 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.25), residues: 1065
  helix:  0.48 (0.29), residues: 273
  sheet:  0.07 (0.29), residues: 324
  loop : -0.32 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 103 
 HIS   0.005   0.001   HIS F 295 
 PHE   0.016   0.002   PHE E 117 
 TYR   0.016   0.001   TYR G  35 
 ARG   0.005   0.000   ARG F 374 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8561 (ttp-170) cc_final: 0.8281 (ttp-170)
REVERT: A  201 ARG cc_start: 0.8495 (mmt180) cc_final: 0.8272 (mmt180)
REVERT: E  141 MET cc_start: 0.8401 (ttt) cc_final: 0.8055 (ttp)
REVERT: E  372 ASN cc_start: 0.6221 (t0) cc_final: 0.5993 (t0)
REVERT: F  279 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7066 (mmtt)
REVERT: G   32 LEU cc_start: 0.7470 (mt) cc_final: 0.7098 (mt)
  outliers start: 18
  outliers final: 7
  residues processed: 107
  average time/residue: 0.9075
  time to fit residues: 106.6938
Evaluate side-chains
  97 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain F residue  343 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 43 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 HIS
E 153 ASN
E 223 ASN
E 350 GLN
F 264 HIS
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  49 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.173665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.135153 restraints weight = 10203.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.17
r_work: 0.3379 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9121  Z= 0.249
  Angle     :  0.586  10.622  12383  Z= 0.302
  Chirality :  0.045   0.146   1452
  Planarity :  0.004   0.057   1519
  Dihedral  :  8.809  73.171   1504
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.52 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.25), residues: 1065
  helix:  0.81 (0.30), residues: 273
  sheet:  0.09 (0.29), residues: 324
  loop : -0.26 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 103 
 HIS   0.006   0.001   HIS F 295 
 PHE   0.018   0.002   PHE E 117 
 TYR   0.016   0.001   TYR G  35 
 ARG   0.004   0.000   ARG E 144 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8565 (ttp-170) cc_final: 0.8239 (ttp-170)
REVERT: E  122 GLN cc_start: 0.8109 (mm110) cc_final: 0.7829 (mt0)
REVERT: E  141 MET cc_start: 0.8430 (ttt) cc_final: 0.8087 (ttp)
REVERT: F  185 LYS cc_start: 0.7169 (tttp) cc_final: 0.6865 (tttt)
REVERT: G   32 LEU cc_start: 0.7610 (mt) cc_final: 0.7172 (mt)
  outliers start: 22
  outliers final: 11
  residues processed: 109
  average time/residue: 0.9683
  time to fit residues: 115.8238
Evaluate side-chains
  102 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   57 MET
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain E residue  244 THR
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain F residue  108 LEU
Chi-restraints excluded: chain F residue  343 ASP
Chi-restraints excluded: chain F residue  413 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 104 optimal weight:    9.9990
   chunk 102 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
E 122 GLN
E 138 HIS
E 153 ASN
E 223 ASN
E 337 GLN
F 264 HIS
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.173177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.134326 restraints weight = 10249.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.24
r_work: 0.3254 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9121  Z= 0.259
  Angle     :  0.584  10.633  12383  Z= 0.302
  Chirality :  0.045   0.144   1452
  Planarity :  0.004   0.054   1519
  Dihedral  :  8.602  72.931   1504
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.14 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1065
  helix:  0.88 (0.30), residues: 278
  sheet:  0.10 (0.28), residues: 324
  loop : -0.21 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 103 
 HIS   0.006   0.001   HIS F 295 
 PHE   0.026   0.002   PHE A 207 
 TYR   0.022   0.002   TYR B 100 
 ARG   0.005   0.000   ARG E 144 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8611 (ttp-170) cc_final: 0.8281 (ttp-170)
REVERT: E  122 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7694 (mt0)
REVERT: E  141 MET cc_start: 0.8451 (ttt) cc_final: 0.8081 (ttp)
REVERT: E  236 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6614 (mp0)
REVERT: E  409 LEU cc_start: 0.8233 (tp) cc_final: 0.8015 (tt)
REVERT: F  374 ARG cc_start: 0.8428 (mtt90) cc_final: 0.8147 (mtt90)
REVERT: G   32 LEU cc_start: 0.7369 (mt) cc_final: 0.6932 (mt)
  outliers start: 24
  outliers final: 15
  residues processed: 101
  average time/residue: 0.8997
  time to fit residues: 99.8745
Evaluate side-chains
  99 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   57 MET
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain E residue  242 THR
Chi-restraints excluded: chain E residue  244 THR
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain E residue  253 ILE
Chi-restraints excluded: chain F residue  108 LEU
Chi-restraints excluded: chain F residue  343 ASP
Chi-restraints excluded: chain F residue  413 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
E 138 HIS
E 153 ASN
E 223 ASN
E 337 GLN
** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 264 HIS
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.171074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.131519 restraints weight = 10232.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.28
r_work: 0.3229 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9121  Z= 0.289
  Angle     :  0.591  10.613  12383  Z= 0.306
  Chirality :  0.045   0.141   1452
  Planarity :  0.004   0.054   1519
  Dihedral  :  8.584  73.205   1504
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.74 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.25), residues: 1065
  helix:  1.00 (0.30), residues: 278
  sheet:  0.11 (0.28), residues: 317
  loop : -0.23 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.006   0.001   HIS F 295 
 PHE   0.019   0.002   PHE E 117 
 TYR   0.016   0.002   TYR G  35 
 ARG   0.007   0.000   ARG E 374 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8221 (ttp-170)
REVERT: E  141 MET cc_start: 0.8467 (ttt) cc_final: 0.8067 (ttp)
REVERT: E  236 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6644 (mp0)
REVERT: E  374 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7539 (mpt-90)
REVERT: F  185 LYS cc_start: 0.7047 (tttp) cc_final: 0.6591 (tttm)
REVERT: F  374 ARG cc_start: 0.8424 (mtt90) cc_final: 0.8155 (mtt90)
  outliers start: 25
  outliers final: 11
  residues processed: 111
  average time/residue: 0.9431
  time to fit residues: 114.4011
Evaluate side-chains
  100 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain B residue  183 MET
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain E residue  244 THR
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain E residue  253 ILE
Chi-restraints excluded: chain F residue  343 ASP
Chi-restraints excluded: chain F residue  413 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    0.1980
   chunk 91 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0980
   chunk 14 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0970
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0980
   overall best weight:    0.2978

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

Flipped N/Q/H residues before XYZ refinement:
E 138 HIS
E 153 ASN
E 223 ASN
E 337 GLN
F 109 HIS
F 264 HIS
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.177250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.138818 restraints weight = 10284.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.29
r_work: 0.3447 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9121  Z= 0.156
  Angle     :  0.537   9.795  12383  Z= 0.279
  Chirality :  0.043   0.142   1452
  Planarity :  0.004   0.054   1519
  Dihedral  :  7.832  71.282   1504
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.26 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.26), residues: 1065
  helix:  1.22 (0.30), residues: 278
  sheet:  0.19 (0.28), residues: 324
  loop : -0.08 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 103 
 HIS   0.006   0.001   HIS F 295 
 PHE   0.018   0.001   PHE A 207 
 TYR   0.019   0.001   TYR B 100 
 ARG   0.008   0.000   ARG E 144 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8495 (t)
REVERT: E  141 MET cc_start: 0.8418 (ttt) cc_final: 0.7890 (ttp)
REVERT: E  144 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.6754 (ptp-110)
REVERT: E  236 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6522 (mp0)
REVERT: E  374 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7621 (mpt-90)
REVERT: F  185 LYS cc_start: 0.7083 (tttp) cc_final: 0.6594 (tttm)
REVERT: F  279 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7186 (mmtt)
  outliers start: 24
  outliers final: 10
  residues processed: 109
  average time/residue: 0.8882
  time to fit residues: 106.7274
Evaluate side-chains
  94 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   57 MET
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain E residue  242 THR
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain E residue  298 LYS
Chi-restraints excluded: chain F residue  108 LEU
Chi-restraints excluded: chain F residue  279 LYS
Chi-restraints excluded: chain F residue  343 ASP
Chi-restraints excluded: chain F residue  413 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0020
   chunk 71 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
E 138 HIS
E 153 ASN
E 223 ASN
E 337 GLN
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.175453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.137094 restraints weight = 10388.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.19
r_work: 0.3341 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9121  Z= 0.222
  Angle     :  0.558  10.248  12383  Z= 0.289
  Chirality :  0.044   0.145   1452
  Planarity :  0.004   0.053   1519
  Dihedral  :  7.848  71.423   1504
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 17.66 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1065
  helix:  1.33 (0.30), residues: 278
  sheet:  0.23 (0.28), residues: 324
  loop : -0.07 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.006   0.001   HIS F 295 
 PHE   0.028   0.002   PHE B 108 
 TYR   0.017   0.002   TYR B 100 
 ARG   0.007   0.000   ARG E 374 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8406 (t)
REVERT: E  141 MET cc_start: 0.8436 (ttt) cc_final: 0.7873 (ttp)
REVERT: E  144 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.6686 (ptp-110)
REVERT: E  236 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6518 (mp0)
REVERT: F  185 LYS cc_start: 0.6985 (tttp) cc_final: 0.6477 (tttm)
REVERT: F  279 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.6988 (mmtt)
  outliers start: 21
  outliers final: 8
  residues processed: 98
  average time/residue: 0.9378
  time to fit residues: 100.6828
Evaluate side-chains
  95 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain E residue  242 THR
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain E residue  298 LYS
Chi-restraints excluded: chain F residue  279 LYS
Chi-restraints excluded: chain F residue  343 ASP
Chi-restraints excluded: chain F residue  413 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0470
   chunk 70 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
E 138 HIS
E 153 ASN
E 223 ASN
E 337 GLN
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.176587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.138690 restraints weight = 10309.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.16
r_work: 0.3358 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9121  Z= 0.190
  Angle     :  0.544  10.137  12383  Z= 0.282
  Chirality :  0.044   0.150   1452
  Planarity :  0.004   0.052   1519
  Dihedral  :  7.697  71.080   1504
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.86 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.26), residues: 1065
  helix:  1.45 (0.30), residues: 278
  sheet:  0.37 (0.28), residues: 331
  loop : -0.18 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.006   0.001   HIS F 295 
 PHE   0.024   0.002   PHE B 108 
 TYR   0.016   0.001   TYR B 100 
 ARG   0.006   0.000   ARG E 144 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8376 (t)
REVERT: E  141 MET cc_start: 0.8416 (ttt) cc_final: 0.7844 (ttp)
REVERT: E  144 ARG cc_start: 0.7370 (ttp-110) cc_final: 0.6717 (ptp-110)
REVERT: E  236 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6476 (mp0)
REVERT: E  285 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7268 (tm-30)
REVERT: F  185 LYS cc_start: 0.6988 (tttp) cc_final: 0.6485 (tttm)
REVERT: F  264 HIS cc_start: 0.7382 (p-80) cc_final: 0.6790 (m90)
REVERT: F  279 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.6968 (mmtt)
  outliers start: 18
  outliers final: 10
  residues processed: 97
  average time/residue: 0.8849
  time to fit residues: 94.5638
Evaluate side-chains
  97 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain E residue  242 THR
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain E residue  285 GLU
Chi-restraints excluded: chain E residue  298 LYS
Chi-restraints excluded: chain F residue  108 LEU
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  279 LYS
Chi-restraints excluded: chain F residue  343 ASP
Chi-restraints excluded: chain F residue  413 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0770
   chunk 0 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
E 138 HIS
E 153 ASN
E 223 ASN
E 337 GLN
E 372 ASN
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.173922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.135675 restraints weight = 10260.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.16
r_work: 0.3267 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9121  Z= 0.241
  Angle     :  0.563  10.209  12383  Z= 0.291
  Chirality :  0.044   0.146   1452
  Planarity :  0.004   0.053   1519
  Dihedral  :  7.823  71.606   1504
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.47 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1065
  helix:  1.48 (0.30), residues: 275
  sheet:  0.27 (0.28), residues: 324
  loop : -0.07 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.007   0.001   HIS F 295 
 PHE   0.023   0.002   PHE B 108 
 TYR   0.015   0.002   TYR B 100 
 ARG   0.006   0.000   ARG E 374 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.8204 (ttp-170)
REVERT: A  131 ARG cc_start: 0.8037 (ttt90) cc_final: 0.7785 (ttt90)
REVERT: A  148 ILE cc_start: 0.8469 (mm) cc_final: 0.8230 (mt)
REVERT: A  175 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8470 (t)
REVERT: E  141 MET cc_start: 0.8469 (ttt) cc_final: 0.7889 (ttp)
REVERT: E  144 ARG cc_start: 0.7396 (ttp-110) cc_final: 0.6666 (ptp-110)
REVERT: E  236 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6527 (mp0)
REVERT: F  185 LYS cc_start: 0.6945 (tttp) cc_final: 0.6501 (tttm)
REVERT: F  279 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.6953 (mmtt)
REVERT: F  338 ASN cc_start: 0.8706 (t0) cc_final: 0.8365 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 101
  average time/residue: 0.9604
  time to fit residues: 106.6780
Evaluate side-chains
  100 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 CYS
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain E residue  242 THR
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain E residue  298 LYS
Chi-restraints excluded: chain F residue  108 LEU
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  279 LYS
Chi-restraints excluded: chain F residue  343 ASP
Chi-restraints excluded: chain F residue  413 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 81 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 59 optimal weight:    0.1980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 108 GLN
A 204 GLN
E 138 HIS
E 153 ASN
E 223 ASN
E 337 GLN
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.174996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.136793 restraints weight = 10300.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.17
r_work: 0.3276 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9121  Z= 0.232
  Angle     :  0.559  10.144  12383  Z= 0.290
  Chirality :  0.044   0.143   1452
  Planarity :  0.004   0.053   1519
  Dihedral  :  7.843  71.662   1504
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.37 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.10 %
    Twisted Proline : 2.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.26), residues: 1065
  helix:  1.52 (0.30), residues: 275
  sheet:  0.25 (0.28), residues: 324
  loop : -0.07 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.007   0.001   HIS F 295 
 PHE   0.023   0.002   PHE B 108 
 TYR   0.016   0.002   TYR B 100 
 ARG   0.005   0.000   ARG E 144 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6376.02 seconds
wall clock time: 113 minutes 40.74 seconds (6820.74 seconds total)