Starting phenix.real_space_refine
on Thu Mar 13 13:21:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y81_39029/03_2025/8y81_39029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y81_39029/03_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_39029/03_2025/8y81_39029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y81_39029/03_2025/8y81_39029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y81_39029/03_2025/8y81_39029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y81_39029/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.78, per 1000 atoms: 0.65
  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: 2.51
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.13
  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: 2.84

  Time building geometry restraints manager: 2.94 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:             1.410
  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:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.670
  Find NCS groups from input model:        0.270
  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:13.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.450
-------------------------------------------------------------------------------
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  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 1.0487
  time to fit residues: 142.8245
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  : 0.952 
-------------------------------------------------------------------------------
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: 0.3117 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
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  : 0.945 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8640 (ttp-170) cc_final: 0.8310 (ttp-170)
REVERT: E  141 MET cc_start: 0.8360 (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: 1.1971
  time to fit residues: 129.3224
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  : 1.177 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 61 optimal weight:    0.4980
   chunk 96 optimal weight:    0.1980
   chunk 43 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 ** 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 = 0.3871 r_free = 0.3871 target = 0.171742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.132063 restraints weight = 10407.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.24
r_work: 0.3278 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9121  Z= 0.210
  Angle     :  0.579  10.589  12383  Z= 0.302
  Chirality :  0.045   0.175   1452
  Planarity :  0.004   0.059   1519
  Dihedral  :  9.459  73.880   1504
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.80 %
    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: -0.11 (0.25), residues: 1065
  helix:  0.47 (0.29), residues: 273
  sheet:  0.04 (0.29), residues: 324
  loop : -0.33 (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 E 144 

*********************** 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
  116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8295 (ttp-170)
REVERT: A  201 ARG cc_start: 0.8484 (mmt180) cc_final: 0.8219 (mmt180)
REVERT: B  100 TYR cc_start: 0.8585 (t80) cc_final: 0.8383 (t80)
REVERT: E  141 MET cc_start: 0.8401 (ttt) cc_final: 0.8065 (ttp)
REVERT: E  372 ASN cc_start: 0.6238 (t0) cc_final: 0.5991 (t0)
REVERT: F  279 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7067 (mmtt)
REVERT: G   32 LEU cc_start: 0.7499 (mt) cc_final: 0.7114 (mt)
  outliers start: 17
  outliers final: 7
  residues processed: 108
  average time/residue: 0.9235
  time to fit residues: 109.3559
Evaluate side-chains
  100 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0270
   chunk 13 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.173680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.135118 restraints weight = 10206.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.23
r_work: 0.3259 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9121  Z= 0.236
  Angle     :  0.579  10.565  12383  Z= 0.300
  Chirality :  0.045   0.151   1452
  Planarity :  0.004   0.057   1519
  Dihedral  :  8.834  73.333   1504
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.52 %
    Favored  : 84.36 %
  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:  0.09 (0.25), residues: 1065
  helix:  0.78 (0.30), residues: 273
  sheet:  0.08 (0.29), residues: 324
  loop : -0.25 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 103 
 HIS   0.005   0.001   HIS F 295 
 PHE   0.016   0.002   PHE A 207 
 TYR   0.015   0.001   TYR G  35 
 ARG   0.004   0.000   ARG F 374 

*********************** 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
  116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.8236 (ttp-170)
REVERT: A  201 ARG cc_start: 0.8430 (mtt180) cc_final: 0.8210 (mmt180)
REVERT: E  122 GLN cc_start: 0.8100 (mm110) cc_final: 0.7768 (mt0)
REVERT: E  141 MET cc_start: 0.8410 (ttt) cc_final: 0.8045 (ttp)
REVERT: E  338 ASN cc_start: 0.8151 (t0) cc_final: 0.7942 (t0)
REVERT: E  372 ASN cc_start: 0.6258 (t0) cc_final: 0.6052 (t0)
REVERT: F  185 LYS cc_start: 0.7047 (tttp) cc_final: 0.6735 (tttt)
REVERT: G   32 LEU cc_start: 0.7413 (mt) cc_final: 0.6992 (mt)
  outliers start: 21
  outliers final: 10
  residues processed: 107
  average time/residue: 0.9106
  time to fit residues: 106.7575
Evaluate side-chains
  100 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 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   32 LEU
Chi-restraints excluded: chain E residue  244 THR
Chi-restraints excluded: chain E residue  246 VAL
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:    0.9990
   chunk 104 optimal weight:   10.0000
   chunk 102 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.172636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.133632 restraints weight = 10260.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.25
r_work: 0.3259 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9121  Z= 0.240
  Angle     :  0.576  10.566  12383  Z= 0.298
  Chirality :  0.045   0.149   1452
  Planarity :  0.004   0.055   1519
  Dihedral  :  8.532  73.088   1504
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.04 %
    Favored  : 82.54 %
  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:  0.19 (0.25), residues: 1065
  helix:  0.96 (0.30), residues: 274
  sheet:  0.10 (0.29), residues: 324
  loop : -0.23 (0.28), residues: 467

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   0.022   0.002   PHE A 207 
 TYR   0.015   0.002   TYR G  35 
 ARG   0.006   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
  115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8602 (ttp-170) cc_final: 0.8266 (ttp-170)
REVERT: A  201 ARG cc_start: 0.8458 (mtt180) cc_final: 0.8246 (mmt180)
REVERT: E  122 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7709 (mt0)
REVERT: E  141 MET cc_start: 0.8439 (ttt) cc_final: 0.8069 (ttp)
REVERT: E  236 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6630 (mp0)
REVERT: E  409 LEU cc_start: 0.8237 (tp) cc_final: 0.8013 (tt)
REVERT: F  374 ARG cc_start: 0.8422 (mtt90) cc_final: 0.8150 (mtt90)
REVERT: G   32 LEU cc_start: 0.7334 (mt) cc_final: 0.6900 (mt)
  outliers start: 24
  outliers final: 13
  residues processed: 105
  average time/residue: 0.8771
  time to fit residues: 101.4521
Evaluate side-chains
  98 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0870
   chunk 22 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0870
   chunk 71 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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
F 264 HIS
** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.175708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.137344 restraints weight = 10211.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.22
r_work: 0.3289 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9121  Z= 0.180
  Angle     :  0.542  10.112  12383  Z= 0.281
  Chirality :  0.044   0.145   1452
  Planarity :  0.004   0.054   1519
  Dihedral  :  7.932  71.298   1504
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.45 %
    Favored  : 81.63 %
  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:  0.37 (0.25), residues: 1065
  helix:  1.13 (0.30), residues: 278
  sheet:  0.21 (0.29), residues: 324
  loop : -0.14 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 103 
 HIS   0.005   0.001   HIS F 295 
 PHE   0.017   0.001   PHE A 207 
 TYR   0.023   0.001   TYR B 100 
 ARG   0.007   0.000   ARG E 144 

*********************** 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
  117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 THR cc_start: 0.8777 (p) cc_final: 0.8464 (t)
REVERT: A  204 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8077 (tp40)
REVERT: E  122 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7719 (mt0)
REVERT: E  141 MET cc_start: 0.8416 (ttt) cc_final: 0.7822 (ttp)
REVERT: E  144 ARG cc_start: 0.7328 (ttp-110) cc_final: 0.6703 (ptp-110)
REVERT: E  236 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6606 (mp0)
REVERT: F  279 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7105 (mmtt)
  outliers start: 19
  outliers final: 9
  residues processed: 107
  average time/residue: 0.8815
  time to fit residues: 103.3380
Evaluate side-chains
  89 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
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 E residue  242 THR
Chi-restraints excluded: chain E residue  244 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    0.4980
   chunk 91 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.4988

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

Flipped N/Q/H residues before XYZ refinement:
A 108 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.169119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.129200 restraints weight = 10350.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.28
r_work: 0.3186 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   9121  Z= 0.435
  Angle     :  0.662  10.943  12383  Z= 0.341
  Chirality :  0.048   0.159   1452
  Planarity :  0.005   0.052   1519
  Dihedral  :  9.081  74.799   1504
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.55 %
    Favored  : 80.73 %
  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:  0.14 (0.25), residues: 1065
  helix:  0.95 (0.30), residues: 284
  sheet:  0.03 (0.28), residues: 318
  loop : -0.26 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 103 
 HIS   0.006   0.001   HIS A 173 
 PHE   0.026   0.003   PHE B 108 
 TYR   0.020   0.002   TYR G  35 
 ARG   0.007   0.001   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
  125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A  212 VAL cc_start: 0.7561 (OUTLIER) cc_final: 0.7351 (p)
REVERT: E  141 MET cc_start: 0.8575 (ttt) cc_final: 0.8211 (ttp)
REVERT: E  236 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6656 (mp0)
REVERT: E  338 ASN cc_start: 0.8343 (t0) cc_final: 0.8081 (t0)
REVERT: F  185 LYS cc_start: 0.6952 (tttp) cc_final: 0.6445 (tttm)
REVERT: F  279 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.6985 (mmtt)
REVERT: F  338 ASN cc_start: 0.8710 (t0) cc_final: 0.8402 (t0)
  outliers start: 27
  outliers final: 13
  residues processed: 116
  average time/residue: 0.9877
  time to fit residues: 125.0158
Evaluate side-chains
  107 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
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 A residue  212 VAL
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  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:    0.7980
   chunk 94 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.172351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.133651 restraints weight = 10410.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.19
r_work: 0.3331 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9121  Z= 0.214
  Angle     :  0.571  13.309  12383  Z= 0.296
  Chirality :  0.044   0.144   1452
  Planarity :  0.004   0.045   1519
  Dihedral  :  8.263  72.480   1504
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.47 %
    Favored  : 79.52 %
  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:  0.29 (0.25), residues: 1065
  helix:  1.16 (0.30), residues: 278
  sheet:  0.04 (0.28), residues: 324
  loop : -0.15 (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   0.020   0.002   PHE A 207 
 TYR   0.021   0.002   TYR B 100 
 ARG   0.007   0.000   ARG E 144 

*********************** 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
  114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 VAL cc_start: 0.7643 (OUTLIER) cc_final: 0.7403 (p)
REVERT: E  141 MET cc_start: 0.8426 (ttt) cc_final: 0.7841 (ttp)
REVERT: E  144 ARG cc_start: 0.7337 (ttp-110) cc_final: 0.6655 (ptp-110)
REVERT: E  236 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6694 (mp0)
REVERT: E  338 ASN cc_start: 0.8300 (t0) cc_final: 0.8056 (t0)
REVERT: F  185 LYS cc_start: 0.7027 (tttp) cc_final: 0.6535 (tttm)
REVERT: F  279 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7010 (mmtt)
REVERT: F  338 ASN cc_start: 0.8711 (t0) cc_final: 0.8372 (t0)
  outliers start: 20
  outliers final: 9
  residues processed: 107
  average time/residue: 0.8303
  time to fit residues: 98.2391
Evaluate side-chains
  104 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
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  212 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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 70 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 93 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.174910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.136909 restraints weight = 10299.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.14
r_work: 0.3335 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2101

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= 0.208
  Angle     :  0.561   8.704  12383  Z= 0.292
  Chirality :  0.044   0.149   1452
  Planarity :  0.004   0.050   1519
  Dihedral  :  7.906  72.178   1504
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.37 %
    Favored  : 79.82 %
  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:  0.41 (0.25), residues: 1065
  helix:  1.30 (0.30), residues: 278
  sheet:  0.12 (0.28), residues: 324
  loop : -0.12 (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   0.019   0.002   PHE B 108 
 TYR   0.014   0.002   TYR G  35 
 ARG   0.007   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
  111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.7953 (ttt90) cc_final: 0.7682 (ttt90)
REVERT: A  175 THR cc_start: 0.8818 (p) cc_final: 0.8486 (t)
REVERT: A  212 VAL cc_start: 0.7567 (OUTLIER) cc_final: 0.7333 (p)
REVERT: E  141 MET cc_start: 0.8423 (ttt) cc_final: 0.7841 (ttp)
REVERT: E  144 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.6635 (ptp-110)
REVERT: E  236 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6575 (mp0)
REVERT: E  298 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8317 (ptpt)
REVERT: F  185 LYS cc_start: 0.6963 (tttp) cc_final: 0.6460 (tttm)
REVERT: F  279 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.6960 (mmtt)
REVERT: F  338 ASN cc_start: 0.8686 (t0) cc_final: 0.8333 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 104
  average time/residue: 0.9369
  time to fit residues: 106.5770
Evaluate side-chains
  102 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
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  212 VAL
Chi-restraints excluded: chain B residue  150 LEU
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  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:    0.2980
   chunk 9 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 55 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0870
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.177246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.139442 restraints weight = 10226.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.14
r_work: 0.3355 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9121  Z= 0.187
  Angle     :  0.555   9.795  12383  Z= 0.288
  Chirality :  0.044   0.148   1452
  Planarity :  0.004   0.050   1519
  Dihedral  :  7.659  71.225   1504
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.07 %
    Favored  : 79.31 %
  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:  0.49 (0.26), residues: 1065
  helix:  1.36 (0.30), residues: 278
  sheet:  0.31 (0.28), residues: 331
  loop : -0.20 (0.30), residues: 456

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   0.020   0.002   PHE A 207 
 TYR   0.026   0.002   TYR B 100 
 ARG   0.007   0.000   ARG E 144 

********************** 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: 16
    poor density    : 92
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8361 (ttp-170) cc_final: 0.8153 (ttp-170)
REVERT: A  131 ARG cc_start: 0.8000 (ttt90) cc_final: 0.7661 (ttt90)
REVERT: A  175 THR cc_start: 0.8760 (p) cc_final: 0.8439 (t)
REVERT: A  212 VAL cc_start: 0.7564 (OUTLIER) cc_final: 0.7330 (p)
REVERT: E  141 MET cc_start: 0.8427 (ttt) cc_final: 0.7852 (ttp)
REVERT: E  144 ARG cc_start: 0.7317 (ttp-110) cc_final: 0.6676 (ptp-110)
REVERT: E  236 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6527 (mp0)
REVERT: E  298 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8293 (ptpt)
REVERT: F  185 LYS cc_start: 0.6983 (tttp) cc_final: 0.6491 (tttm)
REVERT: F  279 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6980 (mmtt)
REVERT: F  338 ASN cc_start: 0.8684 (t0) cc_final: 0.8353 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 103
  average time/residue: 0.8754
  time to fit residues: 99.6670
Evaluate side-chains
  99 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
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  212 VAL
Chi-restraints excluded: chain E residue  244 THR
Chi-restraints excluded: chain E residue  246 VAL
Chi-restraints excluded: chain E residue  298 LYS
Chi-restraints excluded: chain E residue  413 ILE
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:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 59 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   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 204 GLN
E 138 HIS
E 153 ASN
E 337 GLN
E 393 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.174780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.136655 restraints weight = 10300.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.14
r_work: 0.3349 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2185

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= 0.235
  Angle     :  0.566   9.764  12383  Z= 0.293
  Chirality :  0.044   0.142   1452
  Planarity :  0.004   0.051   1519
  Dihedral  :  7.761  71.453   1504
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.47 %
    Favored  : 79.31 %
  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:  0.49 (0.26), residues: 1065
  helix:  1.39 (0.30), residues: 278
  sheet:  0.32 (0.28), residues: 331
  loop : -0.23 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 103 
 HIS   0.007   0.001   HIS F 295 
 PHE   0.020   0.002   PHE E 117 
 TYR   0.023   0.002   TYR B 100 
 ARG   0.007   0.000   ARG E 144 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6924.42 seconds
wall clock time: 120 minutes 41.36 seconds (7241.36 seconds total)