Starting phenix.real_space_refine
on Wed Mar 12 17:24:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u6e_26364/03_2025/7u6e_26364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u6e_26364/03_2025/7u6e_26364.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u6e_26364/03_2025/7u6e_26364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u6e_26364/03_2025/7u6e_26364.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u6e_26364/03_2025/7u6e_26364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u6e_26364/03_2025/7u6e_26364.cif"
  }
  resolution = 3.0
  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=   0.000 sd=   0.002
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      60      5.16       5
     C    5077      2.51       5
     N    1357      2.21       5
     O    1510      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8004
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 163
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
    Chain: "B"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 200
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "E"
      Number of atoms: 4708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4708
          Classifications: {'peptide': 584}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 555}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 2507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2507
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 12, 'TRANS': 295}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 157
          Unusual residues: {'HY1': 1}
          Classifications: {'peptide': 18, 'undetermined': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 16, None: 1}
            Not linked:
              pdbres="HY1 G   0 "
              pdbres="SER G   1 "
    Chain: "H"
      Number of atoms: 157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 157
          Unusual residues: {'HY1': 1}
          Classifications: {'peptide': 18, 'undetermined': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 16, None: 1}
            Not linked:
              pdbres="HY1 H   0 "
              pdbres="SER H   1 "
    Chain: "C"
      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: "E"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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: "F"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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
  Time building chain proxies: 4.95, per 1000 atoms: 0.62
  Number of scatterers: 8004
  At special positions: 0
  Unit cell: (117.307, 86.2133, 83.3866, 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      60     16.00
     O    1510      8.00
     N    1357      7.00
     C    5077      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  11 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS B   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  20 " - pdb=" SG  CYS B  19 " distance=2.01
    Simple disulfide: pdb=" SG  CYS E   8 " - pdb=" SG  CYS E  26 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 126 " - pdb=" SG  CYS E 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 169 " - pdb=" SG  CYS E 188 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 192 " - pdb=" SG  CYS E 201 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 196 " - pdb=" SG  CYS E 207 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 208 " - pdb=" SG  CYS E 216 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 212 " - pdb=" SG  CYS E 225 " distance=2.01
    Simple disulfide: pdb=" SG  CYS E 228 " - pdb=" SG  CYS E 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 241 " - pdb=" SG  CYS E 253 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 259 " - pdb=" SG  CYS E 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 266 " - pdb=" SG  CYS E 274 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 288 " - pdb=" SG  CYS E 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 304 " - pdb=" SG  CYS E 308 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 312 " - pdb=" SG  CYS E 333 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 435 " - pdb=" SG  CYS E 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 524 " - pdb=" SG  CYS F 524 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 312 " - pdb=" SG  CYS F 333 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 435 " - pdb=" SG  CYS F 468 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  11 " - pdb=" SG  CYS G  17 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  11 " - pdb=" SG  CYS H  17 " 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=2, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN E 111 "
      " NAG E1001 " - " ASN E  25 "
      " NAG E1002 " - " ASN E 255 "
      " NAG E1003 " - " ASN E 418 "
      " NAG F1001 " - " ASN F 337 "
      " NAG F1002 " - " ASN F 397 "
      " NAG F1003 " - " ASN F 514 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 841.0 milliseconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 16 sheets defined
      19.9% alpha, 25.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 7
    Processing helix  chain 'A' and resid 12 through 18
    Processing helix  chain 'B' and resid 7 through 19
      removed outlier: 3.775A  pdb=" N   VAL B  12 " --> pdb=" O   GLY B   8 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 16 through 24
      removed outlier: 3.664A  pdb=" N   ARG E  19 " --> pdb=" O   ASN E  16 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 42 through 47
      removed outlier: 3.571A  pdb=" N   PHE E  46 " --> pdb=" O   ARG E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 76
      removed outlier: 4.427A  pdb=" N   LEU E  75 " --> pdb=" O   SER E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 132 through 137
      removed outlier: 3.642A  pdb=" N   ILE E 136 " --> pdb=" O   ASP E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 152
    Processing helix  chain 'E' and resid 255 through 269
    Processing helix  chain 'E' and resid 323 through 329
    Processing helix  chain 'E' and resid 350 through 359
    Processing helix  chain 'E' and resid 435 through 446
      removed outlier: 3.787A  pdb=" N   MET E 442 " --> pdb=" O   GLU E 438 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 496 through 498
      No H-bonds generated for 'chain 'E' and resid 496 through 498'
    Processing helix  chain 'F' and resid 323 through 328
    Processing helix  chain 'F' and resid 329 through 331
      No H-bonds generated for 'chain 'F' and resid 329 through 331'
    Processing helix  chain 'F' and resid 352 through 360
      removed outlier: 3.599A  pdb=" N   ASN F 357 " --> pdb=" O   GLU F 353 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   LEU F 360 " --> pdb=" O   ALA F 356 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 435 through 446
    Processing helix  chain 'F' and resid 496 through 498
      No H-bonds generated for 'chain 'F' and resid 496 through 498'
    Processing helix  chain 'F' and resid 542 through 546
    Processing helix  chain 'F' and resid 691 through 714
    Processing helix  chain 'G' and resid 1 through 13
    Processing helix  chain 'H' and resid 1 through 13
    Processing sheet with id=AA1, first strand: chain 'E' and resid 7 through 14
      removed outlier: 6.709A  pdb=" N   CYS E   8 " --> pdb=" O   GLU E  30 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   HIS E  32 " --> pdb=" O   CYS E   8 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   GLY E  10 " --> pdb=" O   HIS E  32 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   GLN E  34 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ASP E  12 " --> pdb=" O   GLN E  34 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   LEU E  36 " --> pdb=" O   ASP E  12 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG E  14 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   MET E  38 " --> pdb=" O   ARG E  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 14
      removed outlier: 6.709A  pdb=" N   CYS E   8 " --> pdb=" O   GLU E  30 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   HIS E  32 " --> pdb=" O   CYS E   8 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   GLY E  10 " --> pdb=" O   HIS E  32 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   GLN E  34 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ASP E  12 " --> pdb=" O   GLN E  34 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   LEU E  36 " --> pdb=" O   ASP E  12 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG E  14 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   MET E  38 " --> pdb=" O   ARG E  14 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   VAL E  66 " --> pdb=" O   LEU E  37 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ARG E 118 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   VAL E  94 " --> pdb=" O   ARG E 118 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   GLU E 120 " --> pdb=" O   VAL E  94 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   PHE E  96 " --> pdb=" O   GLU E 120 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   VAL E 117 " --> pdb=" O   HIS E 144 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   VAL E 146 " --> pdb=" O   VAL E 117 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ILE E 119 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 171 through 172
      removed outlier: 3.587A  pdb=" N   THR E 172 " --> pdb=" O   VAL E 179 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   VAL E 179 " --> pdb=" O   THR E 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 233
    Processing sheet with id=AA5, first strand: chain 'E' and resid 252 through 254
      removed outlier: 6.543A  pdb=" N   HIS E 247 " --> pdb=" O   CYS E 284 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294
    Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 321
      removed outlier: 10.749A  pdb=" N   VAL E 335 " --> pdb=" O   HIS E 313 " (cutoff:3.500A)
      removed outlier: 11.042A  pdb=" N   LEU E 315 " --> pdb=" O   VAL E 335 " (cutoff:3.500A)
      removed outlier: 10.359A  pdb=" N   ASN E 337 " --> pdb=" O   LEU E 315 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   GLY E 317 " --> pdb=" O   ASN E 337 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 311 through 321
      removed outlier: 10.749A  pdb=" N   VAL E 335 " --> pdb=" O   HIS E 313 " (cutoff:3.500A)
      removed outlier: 11.042A  pdb=" N   LEU E 315 " --> pdb=" O   VAL E 335 " (cutoff:3.500A)
      removed outlier: 10.359A  pdb=" N   ASN E 337 " --> pdb=" O   LEU E 315 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   GLY E 317 " --> pdb=" O   ASN E 337 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   PHE E 427 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   TYR E 401 " --> pdb=" O   PHE E 427 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   HIS E 429 " --> pdb=" O   TYR E 401 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LEU E 403 " --> pdb=" O   HIS E 429 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LEU E 426 " --> pdb=" O   ASP E 456 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 471 through 472
      removed outlier: 6.359A  pdb=" N   GLU E 471 " --> pdb=" O   LYS E 582 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'E' and resid 477 through 480
      removed outlier: 3.517A  pdb=" N   MET E 553 " --> pdb=" O   ILE E 485 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 530 through 534
    Processing sheet with id=AB3, first strand: chain 'F' and resid 311 through 321
      removed outlier: 6.918A  pdb=" N   CYS F 312 " --> pdb=" O   ASN F 337 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   SER F 339 " --> pdb=" O   CYS F 312 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LEU F 314 " --> pdb=" O   SER F 339 " (cutoff:3.500A)
      removed outlier: 11.385A  pdb=" N   ILE F 341 " --> pdb=" O   LEU F 314 " (cutoff:3.500A)
      removed outlier: 12.281A  pdb=" N   GLU F 316 " --> pdb=" O   ILE F 341 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   GLY F 338 " --> pdb=" O   SER F 365 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLY F 366 " --> pdb=" O   ARG F 389 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   GLU F 391 " --> pdb=" O   GLY F 366 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 311 through 321
      removed outlier: 6.918A  pdb=" N   CYS F 312 " --> pdb=" O   ASN F 337 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   SER F 339 " --> pdb=" O   CYS F 312 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LEU F 314 " --> pdb=" O   SER F 339 " (cutoff:3.500A)
      removed outlier: 11.385A  pdb=" N   ILE F 341 " --> pdb=" O   LEU F 314 " (cutoff:3.500A)
      removed outlier: 12.281A  pdb=" N   GLU F 316 " --> pdb=" O   ILE F 341 " (cutoff:3.500A)
      removed outlier: 8.911A  pdb=" N   LYS F 369 " --> pdb=" O   GLY F 338 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU F 340 " --> pdb=" O   LYS F 369 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   ARG F 371 " --> pdb=" O   LEU F 340 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   ILE F 342 " --> pdb=" O   ARG F 371 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   PHE F 427 " --> pdb=" O   SER F 399 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   TYR F 401 " --> pdb=" O   PHE F 427 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   HIS F 429 " --> pdb=" O   TYR F 401 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LEU F 403 " --> pdb=" O   HIS F 429 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 471 through 473
      removed outlier: 5.995A  pdb=" N   GLU F 471 " --> pdb=" O   LYS F 582 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'F' and resid 475 through 480
    Processing sheet with id=AB7, first strand: chain 'F' and resid 532 through 534

    211 hydrogen bonds defined for protein.
    552 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: 2.37

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1333
        1.32 -     1.44: 2277
        1.44 -     1.57: 4505
        1.57 -     1.70: 0
        1.70 -     1.83: 72
  Bond restraints: 8187
  Sorted by residual:
  bond pdb=" C1  NAG F1002 "
       pdb=" O5  NAG F1002 "
    ideal  model  delta    sigma   weight residual
    1.406  1.472 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" C1  NAG E1001 "
       pdb=" O5  NAG E1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.33e+00
  bond pdb=" C1  NAG F1001 "
       pdb=" O5  NAG F1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.00e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" C2  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.532  1.499  0.033 2.00e-02 2.50e+03 2.77e+00
  bond pdb=" CB  ASN E 122 "
       pdb=" CG  ASN E 122 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.14e+00
  ... (remaining 8182 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 10426
        1.84 -     3.67: 571
        3.67 -     5.51: 75
        5.51 -     7.35: 4
        7.35 -     9.18: 3
  Bond angle restraints: 11079
  Sorted by residual:
  angle pdb=" CA  TRP E 559 "
        pdb=" CB  TRP E 559 "
        pdb=" CG  TRP E 559 "
      ideal   model   delta    sigma   weight residual
     113.60  119.95   -6.35 1.90e+00 2.77e-01 1.12e+01
  angle pdb=" N   MET E  56 "
        pdb=" CA  MET E  56 "
        pdb=" C   MET E  56 "
      ideal   model   delta    sigma   weight residual
     108.32  113.08   -4.76 1.64e+00 3.72e-01 8.42e+00
  angle pdb=" N   ILE F 388 "
        pdb=" CA  ILE F 388 "
        pdb=" C   ILE F 388 "
      ideal   model   delta    sigma   weight residual
     108.17  104.16    4.01 1.40e+00 5.10e-01 8.20e+00
  angle pdb=" C5  NAG C   1 "
        pdb=" C4  NAG C   1 "
        pdb=" O4  NAG C   1 "
      ideal   model   delta    sigma   weight residual
     111.70  103.34    8.36 3.00e+00 1.11e-01 7.76e+00
  angle pdb=" N   PHE E 382 "
        pdb=" CA  PHE E 382 "
        pdb=" C   PHE E 382 "
      ideal   model   delta    sigma   weight residual
     109.96  105.83    4.13 1.49e+00 4.50e-01 7.69e+00
  ... (remaining 11074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 4557
       17.44 -    34.89: 373
       34.89 -    52.33: 89
       52.33 -    69.77: 21
       69.77 -    87.22: 12
  Dihedral angle restraints: 5052
    sinusoidal: 2216
      harmonic: 2836
  Sorted by residual:
  dihedral pdb=" CB  CYS E 192 "
           pdb=" SG  CYS E 192 "
           pdb=" SG  CYS E 201 "
           pdb=" CB  CYS E 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.88   81.88     1      1.00e+01 1.00e-02 8.24e+01
  dihedral pdb=" CB  CYS E 288 "
           pdb=" SG  CYS E 288 "
           pdb=" SG  CYS E 301 "
           pdb=" CB  CYS E 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -164.61   78.61     1      1.00e+01 1.00e-02 7.70e+01
  dihedral pdb=" CB  CYS H  11 "
           pdb=" SG  CYS H  11 "
           pdb=" SG  CYS H  17 "
           pdb=" CB  CYS H  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.66  -73.66     1      1.00e+01 1.00e-02 6.90e+01
  ... (remaining 5049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 994
       0.079 -    0.157: 208
       0.157 -    0.236: 16
       0.236 -    0.315: 2
       0.315 -    0.394: 1
  Chirality restraints: 1221
  Sorted by residual:
  chirality pdb=" C1  NAG E1002 "
            pdb=" ND2 ASN E 255 "
            pdb=" C2  NAG E1002 "
            pdb=" O5  NAG E1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" CB  THR F 421 "
            pdb=" CA  THR F 421 "
            pdb=" OG1 THR F 421 "
            pdb=" CG2 THR F 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C1  NAG E1001 "
            pdb=" ND2 ASN E  25 "
            pdb=" C2  NAG E1001 "
            pdb=" O5  NAG E1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 1218 not shown)

  Planarity restraints: 1423
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN E 255 "    0.029 2.00e-02 2.50e+03   2.94e-02 1.08e+01
        pdb=" CG  ASN E 255 "   -0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASN E 255 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN E 255 "   -0.043 2.00e-02 2.50e+03
        pdb=" C1  NAG E1002 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 717 "    0.216 9.50e-02 1.11e+02   9.76e-02 7.29e+00
        pdb=" NE  ARG F 717 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 717 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 717 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 717 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 345 "   -0.212 9.50e-02 1.11e+02   9.56e-02 6.59e+00
        pdb=" NE  ARG F 345 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 345 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 345 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 345 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1420 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 418
        2.72 -     3.26: 8223
        3.26 -     3.81: 13796
        3.81 -     4.35: 18306
        4.35 -     4.90: 29626
  Nonbonded interactions: 70369
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU E 211 "
            pdb=" ND2 ASN E 230 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" O3  NAG E1002 "
            pdb=" O7  NAG E1002 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OE2 GLU E 120 "
            pdb=" NZ  LYS E 121 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" OH  TYR F 398 "
            pdb=" OD2 ASP F 456 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OE2 GLU E 471 "
            pdb=" OH  TYR E 492 "
     model   vdw
     2.357 3.040
  ... (remaining 70364 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 'G'
  selection = chain 'H'
}

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:             1.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.610
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
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      :  0.008   0.066   8187  Z= 0.542
  Angle     :  0.914   9.183  11079  Z= 0.496
  Chirality :  0.061   0.394   1221
  Planarity :  0.008   0.098   1416
  Dihedral  : 14.187  87.215   3150
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.61 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  8.29 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -2.19 (0.24), residues: 954
  helix: -1.27 (0.37), residues: 182
  sheet: -1.55 (0.42), residues: 148
  loop : -1.53 (0.22), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP F 414 
 HIS   0.012   0.002   HIS E 144 
 PHE   0.042   0.004   PHE E  89 
 TYR   0.025   0.004   TYR F 507 
 ARG   0.021   0.002   ARG F 717 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 190
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: E  299 LEU cc_start: 0.7723 (tp) cc_final: 0.7523 (tp)
REVERT: E  483 ASP cc_start: 0.6432 (p0) cc_final: 0.6142 (p0)
REVERT: E  505 LEU cc_start: 0.7781 (tt) cc_final: 0.7518 (tp)
REVERT: E  553 MET cc_start: 0.7061 (mpp) cc_final: 0.6748 (mpp)
REVERT: F  318 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6641 (tp30)
REVERT: F  423 GLN cc_start: 0.8025 (tp40) cc_final: 0.7755 (tp-100)
REVERT: F  579 TYR cc_start: 0.7289 (m-80) cc_final: 0.6999 (m-80)
  outliers start: 16
  outliers final: 3
  residues processed: 198
  average time/residue: 1.2700
  time to fit residues: 265.6224
Evaluate side-chains
  99 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  201 CYS
Chi-restraints excluded: chain E residue  250 ASP
Chi-restraints excluded: chain F residue  412 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0060
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 264 HIS
E 343 ASN
E 348 ASN
E 417 HIS
** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 405 ASN
F 548 HIS
F 561 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.161627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.144614 restraints weight = 12862.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4227 rms_B_bonded: 2.06
r_work: 0.4115 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3983 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8187  Z= 0.291
  Angle     :  0.768  13.217  11079  Z= 0.403
  Chirality :  0.050   0.329   1221
  Planarity :  0.004   0.039   1416
  Dihedral  :  8.014  54.582   1237
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.00 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.69 (0.25), residues: 954
  helix: -0.51 (0.39), residues: 173
  sheet: -1.16 (0.42), residues: 159
  loop : -1.32 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F 559 
 HIS   0.007   0.001   HIS E 275 
 PHE   0.032   0.003   PHE E 482 
 TYR   0.017   0.002   TYR E  60 
 ARG   0.005   0.001   ARG E 454 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 GLU cc_start: 0.7549 (mp0) cc_final: 0.7051 (mp0)
REVERT: E  110 MET cc_start: 0.8034 (mmp) cc_final: 0.7241 (mmt)
REVERT: E  483 ASP cc_start: 0.7030 (p0) cc_final: 0.6764 (p0)
REVERT: E  553 MET cc_start: 0.7125 (mpp) cc_final: 0.6750 (mpp)
REVERT: F  318 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6911 (tp30)
REVERT: F  350 LEU cc_start: 0.3938 (OUTLIER) cc_final: 0.3729 (tt)
REVERT: F  521 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6949 (tm-30)
REVERT: F  579 TYR cc_start: 0.7739 (m-80) cc_final: 0.7352 (m-80)
REVERT: G    8 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8095 (pp30)
  outliers start: 32
  outliers final: 6
  residues processed: 131
  average time/residue: 1.1105
  time to fit residues: 155.9472
Evaluate side-chains
  93 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  201 CYS
Chi-restraints excluded: chain E residue  300 LEU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain F residue  350 LEU
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  521 GLN
Chi-restraints excluded: chain F residue  693 LEU
Chi-restraints excluded: chain F residue  696 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0170
   chunk 30 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 87 optimal weight:    0.4980
   chunk 0 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0370
   overall best weight:    0.2496

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 295 ASN
E 348 ASN
E 513 GLN
E 561 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.162836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.146254 restraints weight = 12928.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.4257 rms_B_bonded: 2.05
r_work: 0.4145 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.4015 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8187  Z= 0.208
  Angle     :  0.670  10.111  11079  Z= 0.347
  Chirality :  0.047   0.282   1221
  Planarity :  0.004   0.038   1416
  Dihedral  :  7.324  51.679   1235
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.71 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.59 (0.25), residues: 954
  helix: -0.57 (0.38), residues: 173
  sheet: -1.13 (0.40), residues: 165
  loop : -1.19 (0.23), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 559 
 HIS   0.008   0.001   HIS E 263 
 PHE   0.021   0.002   PHE F 705 
 TYR   0.013   0.001   TYR E  60 
 ARG   0.010   0.001   ARG E 498 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 GLU cc_start: 0.7488 (mp0) cc_final: 0.6948 (mp0)
REVERT: E   44 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7786 (mm-30)
REVERT: E   73 LYS cc_start: 0.8047 (pttp) cc_final: 0.7833 (pptt)
REVERT: E   86 ARG cc_start: 0.6990 (mtm-85) cc_final: 0.6720 (ttm-80)
REVERT: E  110 MET cc_start: 0.7991 (mmp) cc_final: 0.7272 (mmt)
REVERT: E  297 SER cc_start: 0.6910 (m) cc_final: 0.6681 (p)
REVERT: E  355 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7295 (tp30)
REVERT: E  406 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7210 (mm-40)
REVERT: E  426 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7723 (mt)
REVERT: E  483 ASP cc_start: 0.6923 (p0) cc_final: 0.6673 (p0)
REVERT: E  553 MET cc_start: 0.6617 (mpp) cc_final: 0.6277 (mpp)
REVERT: F  350 LEU cc_start: 0.4142 (OUTLIER) cc_final: 0.3673 (tt)
REVERT: F  442 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7087 (ttp)
REVERT: F  579 TYR cc_start: 0.7708 (m-80) cc_final: 0.7306 (m-80)
REVERT: F  706 GLU cc_start: 0.7775 (tt0) cc_final: 0.7250 (pt0)
REVERT: G    8 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7871 (pp30)
REVERT: H    2 LEU cc_start: 0.7663 (mp) cc_final: 0.7425 (mp)
  outliers start: 31
  outliers final: 10
  residues processed: 117
  average time/residue: 0.9972
  time to fit residues: 125.1958
Evaluate side-chains
  94 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   44 GLU
Chi-restraints excluded: chain E residue  201 CYS
Chi-restraints excluded: chain E residue  300 LEU
Chi-restraints excluded: chain E residue  355 GLU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain E residue  426 LEU
Chi-restraints excluded: chain F residue  324 VAL
Chi-restraints excluded: chain F residue  350 LEU
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  433 LYS
Chi-restraints excluded: chain F residue  442 MET
Chi-restraints excluded: chain F residue  571 THR
Chi-restraints excluded: chain F residue  578 THR
Chi-restraints excluded: chain F residue  696 LEU
Chi-restraints excluded: chain G residue    1 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 80 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.158965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.142243 restraints weight = 12899.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 2.05
r_work: 0.4093 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3960 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8187  Z= 0.308
  Angle     :  0.693   7.084  11079  Z= 0.358
  Chirality :  0.049   0.312   1221
  Planarity :  0.004   0.042   1416
  Dihedral  :  7.314  52.706   1235
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.96 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.70 (0.26), residues: 954
  helix: -0.49 (0.40), residues: 173
  sheet: -1.26 (0.40), residues: 165
  loop : -1.31 (0.23), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E 551 
 HIS   0.006   0.001   HIS E 144 
 PHE   0.025   0.003   PHE E  89 
 TYR   0.020   0.002   TYR E  60 
 ARG   0.006   0.001   ARG E 498 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
REVERT: A    4 GLU cc_start: 0.7554 (mp0) cc_final: 0.6982 (mp0)
REVERT: E   44 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7833 (mm-30)
REVERT: E  355 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7326 (tp30)
REVERT: E  406 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7153 (mm-40)
REVERT: E  426 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7757 (mt)
REVERT: F  382 PHE cc_start: 0.8141 (m-80) cc_final: 0.7914 (m-80)
REVERT: F  579 TYR cc_start: 0.7739 (m-80) cc_final: 0.7315 (m-80)
REVERT: F  706 GLU cc_start: 0.7693 (tt0) cc_final: 0.7160 (pt0)
REVERT: G    8 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8157 (pp30)
  outliers start: 29
  outliers final: 12
  residues processed: 101
  average time/residue: 1.0638
  time to fit residues: 115.2494
Evaluate side-chains
  91 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   44 GLU
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  201 CYS
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  300 LEU
Chi-restraints excluded: chain E residue  355 GLU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain E residue  426 LEU
Chi-restraints excluded: chain F residue  324 VAL
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  559 TRP
Chi-restraints excluded: chain F residue  571 THR
Chi-restraints excluded: chain F residue  578 THR
Chi-restraints excluded: chain F residue  696 LEU
Chi-restraints excluded: chain G residue    1 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0020
   chunk 89 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 513 GLN
E 561 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.158751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.142004 restraints weight = 12850.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 2.04
r_work: 0.4094 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3961 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   8187  Z= 0.289
  Angle     :  0.667   7.315  11079  Z= 0.344
  Chirality :  0.048   0.303   1221
  Planarity :  0.004   0.052   1416
  Dihedral  :  7.138  52.918   1235
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 19.30 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.74 (0.25), residues: 954
  helix: -0.41 (0.40), residues: 173
  sheet: -1.27 (0.40), residues: 159
  loop : -1.39 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 551 
 HIS   0.004   0.001   HIS E 144 
 PHE   0.019   0.002   PHE E  89 
 TYR   0.017   0.002   TYR E  60 
 ARG   0.011   0.001   ARG E 498 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   44 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7818 (mm-30)
REVERT: E   73 LYS cc_start: 0.7876 (pttp) cc_final: 0.7663 (pmtt)
REVERT: E  355 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7326 (tp30)
REVERT: E  406 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7212 (mm-40)
REVERT: E  426 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7778 (mt)
REVERT: F  350 LEU cc_start: 0.4272 (OUTLIER) cc_final: 0.3797 (tt)
REVERT: F  382 PHE cc_start: 0.8165 (m-80) cc_final: 0.7941 (m-80)
REVERT: F  417 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6861 (t70)
REVERT: F  579 TYR cc_start: 0.7708 (m-80) cc_final: 0.7284 (m-80)
REVERT: F  706 GLU cc_start: 0.7672 (tt0) cc_final: 0.7094 (pt0)
REVERT: G    8 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8235 (pp30)
  outliers start: 33
  outliers final: 11
  residues processed: 103
  average time/residue: 1.1724
  time to fit residues: 129.8235
Evaluate side-chains
  89 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 1.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   44 GLU
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  355 GLU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain E residue  426 LEU
Chi-restraints excluded: chain F residue  324 VAL
Chi-restraints excluded: chain F residue  350 LEU
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  417 HIS
Chi-restraints excluded: chain F residue  559 TRP
Chi-restraints excluded: chain F residue  571 THR
Chi-restraints excluded: chain F residue  578 THR
Chi-restraints excluded: chain F residue  696 LEU
Chi-restraints excluded: chain G residue    1 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 74 optimal weight:    0.0070
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 80 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.3798

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.160616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.144063 restraints weight = 12807.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.4227 rms_B_bonded: 2.02
r_work: 0.4117 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3985 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8187  Z= 0.209
  Angle     :  0.623  10.234  11079  Z= 0.319
  Chirality :  0.046   0.301   1221
  Planarity :  0.004   0.045   1416
  Dihedral  :  6.795  50.778   1234
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 20.20 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.62 (0.26), residues: 954
  helix: -0.24 (0.40), residues: 173
  sheet: -1.26 (0.40), residues: 159
  loop : -1.30 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 551 
 HIS   0.004   0.001   HIS E 185 
 PHE   0.015   0.002   PHE F 705 
 TYR   0.013   0.001   TYR E  60 
 ARG   0.011   0.001   ARG E 409 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 87
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: E   44 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7783 (mm-30)
REVERT: E  355 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7338 (tp30)
REVERT: E  406 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7309 (mm-40)
REVERT: E  426 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7790 (mt)
REVERT: F  350 LEU cc_start: 0.4224 (OUTLIER) cc_final: 0.3860 (tt)
REVERT: F  382 PHE cc_start: 0.8192 (m-80) cc_final: 0.7977 (m-80)
REVERT: F  579 TYR cc_start: 0.7657 (m-80) cc_final: 0.7253 (m-80)
REVERT: G    8 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8262 (pp30)
REVERT: H   10 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6141 (tt0)
  outliers start: 33
  outliers final: 11
  residues processed: 105
  average time/residue: 1.2851
  time to fit residues: 143.8968
Evaluate side-chains
  92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue   44 GLU
Chi-restraints excluded: chain E residue  257 SER
Chi-restraints excluded: chain E residue  355 GLU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain E residue  426 LEU
Chi-restraints excluded: chain E residue  553 MET
Chi-restraints excluded: chain F residue  324 VAL
Chi-restraints excluded: chain F residue  350 LEU
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  480 THR
Chi-restraints excluded: chain F residue  559 TRP
Chi-restraints excluded: chain F residue  571 THR
Chi-restraints excluded: chain F residue  696 LEU
Chi-restraints excluded: chain G residue    1 SER
Chi-restraints excluded: chain H residue   10 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0470
   chunk 61 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.160375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.143512 restraints weight = 12946.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 2.05
r_work: 0.4102 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3971 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8187  Z= 0.247
  Angle     :  0.640   9.184  11079  Z= 0.328
  Chirality :  0.046   0.304   1221
  Planarity :  0.004   0.076   1416
  Dihedral  :  6.790  51.515   1234
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 21.79 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.65 (0.26), residues: 954
  helix: -0.32 (0.40), residues: 175
  sheet: -1.22 (0.41), residues: 157
  loop : -1.33 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 551 
 HIS   0.004   0.001   HIS E 185 
 PHE   0.019   0.002   PHE E 482 
 TYR   0.015   0.001   TYR E  60 
 ARG   0.016   0.001   ARG E 498 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: E  355 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7352 (tp30)
REVERT: E  406 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7287 (mm-40)
REVERT: E  426 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7773 (mt)
REVERT: F  350 LEU cc_start: 0.4215 (OUTLIER) cc_final: 0.3867 (tt)
REVERT: F  417 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.6460 (t70)
REVERT: F  579 TYR cc_start: 0.7607 (m-80) cc_final: 0.7185 (m-80)
REVERT: G    8 GLN cc_start: 0.8542 (tm-30) cc_final: 0.7902 (pp30)
  outliers start: 27
  outliers final: 12
  residues processed: 101
  average time/residue: 1.4521
  time to fit residues: 158.6068
Evaluate side-chains
  92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue  257 SER
Chi-restraints excluded: chain E residue  355 GLU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain E residue  426 LEU
Chi-restraints excluded: chain E residue  553 MET
Chi-restraints excluded: chain F residue  324 VAL
Chi-restraints excluded: chain F residue  350 LEU
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  417 HIS
Chi-restraints excluded: chain F residue  480 THR
Chi-restraints excluded: chain F residue  559 TRP
Chi-restraints excluded: chain F residue  578 THR
Chi-restraints excluded: chain F residue  696 LEU
Chi-restraints excluded: chain H residue   10 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
E 521 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.157569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.141015 restraints weight = 13099.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 2.03
r_work: 0.4080 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3946 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8187  Z= 0.294
  Angle     :  0.680  11.265  11079  Z= 0.345
  Chirality :  0.047   0.315   1221
  Planarity :  0.004   0.058   1416
  Dihedral  :  6.959  53.246   1234
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 21.68 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.74 (0.26), residues: 954
  helix: -0.37 (0.40), residues: 173
  sheet: -1.31 (0.40), residues: 162
  loop : -1.38 (0.23), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP E 551 
 HIS   0.004   0.001   HIS B  10 
 PHE   0.022   0.002   PHE E  89 
 TYR   0.017   0.002   TYR E  60 
 ARG   0.012   0.001   ARG E 409 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 77
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
REVERT: E  355 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7337 (tp30)
REVERT: E  406 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7308 (mm-40)
REVERT: E  426 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7828 (mt)
REVERT: F  579 TYR cc_start: 0.7713 (m-80) cc_final: 0.7310 (m-80)
  outliers start: 35
  outliers final: 11
  residues processed: 100
  average time/residue: 0.9951
  time to fit residues: 107.5024
Evaluate side-chains
  85 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue  257 SER
Chi-restraints excluded: chain E residue  355 GLU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain E residue  426 LEU
Chi-restraints excluded: chain E residue  553 MET
Chi-restraints excluded: chain F residue  324 VAL
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  480 THR
Chi-restraints excluded: chain F residue  559 TRP
Chi-restraints excluded: chain F residue  578 THR
Chi-restraints excluded: chain H residue   10 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0040
   chunk 66 optimal weight:    3.9990
   chunk 55 optimal weight:    0.3980
   chunk 50 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.4792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.158839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.142152 restraints weight = 13096.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 2.05
r_work: 0.4093 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3960 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8187  Z= 0.256
  Angle     :  0.682  10.794  11079  Z= 0.346
  Chirality :  0.047   0.307   1221
  Planarity :  0.005   0.084   1416
  Dihedral  :  6.925  52.218   1234
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 22.59 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.74 (0.26), residues: 954
  helix: -0.46 (0.40), residues: 172
  sheet: -1.28 (0.40), residues: 162
  loop : -1.35 (0.23), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP E 551 
 HIS   0.004   0.001   HIS E 185 
 PHE   0.017   0.002   PHE E  89 
 TYR   0.014   0.001   TYR E  60 
 ARG   0.019   0.001   ARG E 498 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: E  250 ASP cc_start: 0.6387 (t0) cc_final: 0.6037 (t0)
REVERT: E  355 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7434 (tp30)
REVERT: E  406 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7295 (mm-40)
REVERT: E  426 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7830 (mt)
REVERT: F  579 TYR cc_start: 0.7696 (m-80) cc_final: 0.7304 (m-80)
REVERT: F  706 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7058 (pt0)
  outliers start: 24
  outliers final: 12
  residues processed: 91
  average time/residue: 1.0898
  time to fit residues: 107.0174
Evaluate side-chains
  87 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue  188 CYS
Chi-restraints excluded: chain E residue  257 SER
Chi-restraints excluded: chain E residue  355 GLU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain E residue  426 LEU
Chi-restraints excluded: chain E residue  474 LYS
Chi-restraints excluded: chain E residue  553 MET
Chi-restraints excluded: chain F residue  324 VAL
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  480 THR
Chi-restraints excluded: chain F residue  559 TRP
Chi-restraints excluded: chain F residue  706 GLU
Chi-restraints excluded: chain H residue   10 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 80 optimal weight:    0.3980
   chunk 90 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0980
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0970
   overall best weight:    0.4378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.159440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.142812 restraints weight = 12943.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 2.04
r_work: 0.4102 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3970 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8187  Z= 0.238
  Angle     :  0.674  10.622  11079  Z= 0.340
  Chirality :  0.046   0.300   1221
  Planarity :  0.004   0.062   1416
  Dihedral  :  6.812  51.186   1234
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.16 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.80 (0.26), residues: 954
  helix: -0.57 (0.39), residues: 174
  sheet: -1.29 (0.40), residues: 162
  loop : -1.39 (0.23), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP E 551 
 HIS   0.004   0.001   HIS E 185 
 PHE   0.017   0.002   PHE E  89 
 TYR   0.013   0.001   TYR E  60 
 ARG   0.014   0.001   ARG E 409 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
REVERT: E  250 ASP cc_start: 0.6390 (t0) cc_final: 0.6081 (t0)
REVERT: E  355 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7440 (tp30)
REVERT: E  406 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7299 (mm-40)
REVERT: E  426 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7842 (mt)
REVERT: F  579 TYR cc_start: 0.7642 (m-80) cc_final: 0.7377 (m-80)
  outliers start: 20
  outliers final: 14
  residues processed: 90
  average time/residue: 1.0315
  time to fit residues: 99.9870
Evaluate side-chains
  88 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue  188 CYS
Chi-restraints excluded: chain E residue  196 CYS
Chi-restraints excluded: chain E residue  257 SER
Chi-restraints excluded: chain E residue  355 GLU
Chi-restraints excluded: chain E residue  377 VAL
Chi-restraints excluded: chain E residue  426 LEU
Chi-restraints excluded: chain E residue  474 LYS
Chi-restraints excluded: chain F residue  324 VAL
Chi-restraints excluded: chain F residue  412 TRP
Chi-restraints excluded: chain F residue  480 THR
Chi-restraints excluded: chain F residue  559 TRP
Chi-restraints excluded: chain F residue  569 LEU
Chi-restraints excluded: chain F residue  578 THR
Chi-restraints excluded: chain H residue   10 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 52 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   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 348 ASN
E 513 GLN
E 561 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.158537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.141958 restraints weight = 12995.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.4206 rms_B_bonded: 2.03
r_work: 0.4093 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3960 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8187  Z= 0.273
  Angle     :  0.686  11.159  11079  Z= 0.348
  Chirality :  0.047   0.300   1221
  Planarity :  0.005   0.089   1416
  Dihedral  :  6.858  51.402   1234
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.70 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -1.86 (0.25), residues: 954
  helix: -0.55 (0.39), residues: 174
  sheet: -1.31 (0.40), residues: 162
  loop : -1.46 (0.23), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP E 551 
 HIS   0.006   0.001   HIS E 144 
 PHE   0.023   0.002   PHE F 572 
 TYR   0.014   0.001   TYR E  60 
 ARG   0.021   0.001   ARG E 498 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5847.27 seconds
wall clock time: 102 minutes 51.52 seconds (6171.52 seconds total)