Starting phenix.real_space_refine
on Fri Jul 25 21:40:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lup_63401/07_2025/9lup_63401.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lup_63401/07_2025/9lup_63401.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lup_63401/07_2025/9lup_63401.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lup_63401/07_2025/9lup_63401.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lup_63401/07_2025/9lup_63401.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lup_63401/07_2025/9lup_63401.cif"
  }
  resolution = 2.8
  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=   1.040
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      38      5.16       5
     C    5133      2.51       5
     N    1394      2.21       5
     O    1516      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8081
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3403
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 16, 'TRANS': 421}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2647
          Classifications: {'peptide': 334}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 315}
    Chain: "C"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 907
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 3, 'TRANS': 107}
    Chain: "D"
      Number of atoms: 1099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1099
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'GA3': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.83, per 1000 atoms: 0.72
  Number of scatterers: 8081
  At special positions: 0
  Unit cell: (73.7649, 96.1179, 125.177, 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      38     16.00
     O    1516      8.00
     N    1394      7.00
     C    5133      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.01
  Conformation dependent library (CDL) restraints added in 924.4 milliseconds
  

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 5 sheets defined
      58.3% alpha, 13.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 58 through 87
      removed outlier: 7.102A  pdb=" N   GLU A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   ASP A  79 " --> pdb=" O   ASN A  75 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   GLY A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 108
    Processing helix  chain 'A' and resid 215 through 234
      removed outlier: 3.731A  pdb=" N   VAL A 219 " --> pdb=" O   GLN A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 254
      removed outlier: 3.917A  pdb=" N   ALA A 242 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 252 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   SER A 253 " --> pdb=" O   CYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 274
      removed outlier: 4.172A  pdb=" N   LYS A 260 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   TYR A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 295
    Processing helix  chain 'A' and resid 300 through 317
      removed outlier: 3.718A  pdb=" N   ALA A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 3.765A  pdb=" N   LEU A 339 " --> pdb=" O   GLN A 335 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.835A  pdb=" N   HIS A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 382 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 400
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 3.641A  pdb=" N   MET A 404 " --> pdb=" O   ASP A 401 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A 405 " --> pdb=" O   ALA A 402 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLU A 406 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 401 through 406'
    Processing helix  chain 'A' and resid 422 through 427
      removed outlier: 3.567A  pdb=" N   LEU A 427 " --> pdb=" O   HIS A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 444
      removed outlier: 3.530A  pdb=" N   LYS A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LYS A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN A 442 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 480
    Processing helix  chain 'A' and resid 486 through 505
      removed outlier: 3.519A  pdb=" N   VAL A 504 " --> pdb=" O   ILE A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 511
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 536 through 550
      removed outlier: 3.657A  pdb=" N   SER A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   PHE A 550 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 34
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 126 through 139
      removed outlier: 3.510A  pdb=" N   LEU B 130 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 170
      removed outlier: 3.567A  pdb=" N   TRP B 163 " --> pdb=" O   TYR B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 5.755A  pdb=" N   TRP B 174 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS B 176 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 207
    Processing helix  chain 'B' and resid 227 through 233
    Processing helix  chain 'B' and resid 240 through 252
    Processing helix  chain 'B' and resid 291 through 304
    Processing helix  chain 'B' and resid 320 through 324
      removed outlier: 3.530A  pdb=" N   LEU B 323 " --> pdb=" O   GLY B 320 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU B 324 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 320 through 324'
    Processing helix  chain 'B' and resid 327 through 342
      removed outlier: 3.671A  pdb=" N   HIS B 331 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 35
    Processing helix  chain 'C' and resid 36 through 45
    Processing helix  chain 'C' and resid 48 through 56
    Processing helix  chain 'C' and resid 59 through 67
    Processing helix  chain 'C' and resid 68 through 79
      removed outlier: 3.693A  pdb=" N   TRP C  72 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   HIS C  79 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 97
    Processing helix  chain 'C' and resid 99 through 107
      removed outlier: 3.860A  pdb=" N   TYR C 107 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 113
    Processing helix  chain 'C' and resid 122 through 141
      removed outlier: 4.208A  pdb=" N   SER C 141 " --> pdb=" O   TYR C 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 25
    Processing helix  chain 'D' and resid 27 through 33
    Processing helix  chain 'D' and resid 49 through 68
    Processing helix  chain 'D' and resid 89 through 103
      removed outlier: 3.784A  pdb=" N   LYS D 103 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 120
    Processing helix  chain 'D' and resid 121 through 137
    Processing helix  chain 'D' and resid 140 through 148
      removed outlier: 3.648A  pdb=" N   ILE D 144 " --> pdb=" O   THR D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 166
      removed outlier: 3.581A  pdb=" N   ASN D 166 " --> pdb=" O   VAL D 162 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211
      removed outlier: 4.388A  pdb=" N   LEU B  77 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL B 141 " --> pdb=" O   PRO B 107 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL B 108 " --> pdb=" O   PHE B 186 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   ALA B 188 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   LEU B 110 " --> pdb=" O   ALA B 188 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   ASP B 190 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   PHE B 112 " --> pdb=" O   ASP B 190 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   ILE B 185 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
      removed outlier: 8.622A  pdb=" N   ILE B 215 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU B 187 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   LEU B 217 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLY B 189 " --> pdb=" O   LEU B 217 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   SER B 281 " --> pdb=" O   LYS B 310 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   MET B 312 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL B 283 " --> pdb=" O   MET B 312 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   LEU B 314 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL B 285 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 390
      removed outlier: 7.090A  pdb=" N   ARG A 322 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 8.433A  pdb=" N   ALA A 416 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   HIS A 324 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ASN A 418 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 418 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   VAL A 420 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ILE A 447 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ALA A 579 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390
      removed outlier: 7.090A  pdb=" N   ARG A 322 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 8.433A  pdb=" N   ALA A 416 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   HIS A 324 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ASN A 418 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 418 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   VAL A 420 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ILE A 447 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 5.843A  pdb=" N   TRP A 569 " --> pdb=" O   PRO A 573 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 35 through 36
      removed outlier: 3.787A  pdb=" N   THR B  40 " --> pdb=" O   ARG B  36 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 10

    450 hydrogen bonds defined for protein.
    1317 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: 2.22

  Time building geometry restraints manager: 2.38 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1448
        1.32 -     1.44: 2094
        1.44 -     1.57: 4655
        1.57 -     1.69: 0
        1.69 -     1.81: 59
  Bond restraints: 8256
  Sorted by residual:
  bond pdb=" C10 GA3 B 401 "
       pdb=" C9  GA3 B 401 "
    ideal  model  delta    sigma   weight residual
    1.506  1.560 -0.054 2.00e-02 2.50e+03 7.36e+00
  bond pdb=" C7  GA3 B 401 "
       pdb=" O71 GA3 B 401 "
    ideal  model  delta    sigma   weight residual
    1.247  1.215  0.032 2.00e-02 2.50e+03 2.54e+00
  bond pdb=" C7  GA3 B 401 "
       pdb=" O72 GA3 B 401 "
    ideal  model  delta    sigma   weight residual
    1.248  1.217  0.031 2.00e-02 2.50e+03 2.35e+00
  bond pdb=" C13 GA3 B 401 "
       pdb=" C14 GA3 B 401 "
    ideal  model  delta    sigma   weight residual
    1.519  1.548 -0.029 2.00e-02 2.50e+03 2.13e+00
  bond pdb=" CG  PRO D 156 "
       pdb=" CD  PRO D 156 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.71e+00
  ... (remaining 8251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 10954
        1.64 -     3.27: 189
        3.27 -     4.91: 44
        4.91 -     6.54: 5
        6.54 -     8.18: 4
  Bond angle restraints: 11196
  Sorted by residual:
  angle pdb=" N   TRP A 336 "
        pdb=" CA  TRP A 336 "
        pdb=" C   TRP A 336 "
      ideal   model   delta    sigma   weight residual
     109.81  115.96   -6.15 2.21e+00 2.05e-01 7.74e+00
  angle pdb=" CA  PRO D 156 "
        pdb=" N   PRO D 156 "
        pdb=" CD  PRO D 156 "
      ideal   model   delta    sigma   weight residual
     112.00  108.43    3.57 1.40e+00 5.10e-01 6.51e+00
  angle pdb=" C10 GA3 B 401 "
        pdb=" C5  GA3 B 401 "
        pdb=" C6  GA3 B 401 "
      ideal   model   delta    sigma   weight residual
     106.02   98.62    7.40 3.00e+00 1.11e-01 6.09e+00
  angle pdb=" CB  GLU C  42 "
        pdb=" CG  GLU C  42 "
        pdb=" CD  GLU C  42 "
      ideal   model   delta    sigma   weight residual
     112.60  116.74   -4.14 1.70e+00 3.46e-01 5.93e+00
  angle pdb=" C   LYS D 139 "
        pdb=" N   THR D 140 "
        pdb=" CA  THR D 140 "
      ideal   model   delta    sigma   weight residual
     121.80  127.60   -5.80 2.44e+00 1.68e-01 5.64e+00
  ... (remaining 11191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.01: 4274
       18.01 -    36.02: 530
       36.02 -    54.04: 164
       54.04 -    72.05: 32
       72.05 -    90.06: 14
  Dihedral angle restraints: 5014
    sinusoidal: 2058
      harmonic: 2956
  Sorted by residual:
  dihedral pdb=" CA  ARG A 271 "
           pdb=" C   ARG A 271 "
           pdb=" N   ARG A 272 "
           pdb=" CA  ARG A 272 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.55   22.45     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CG  ARG B  73 "
           pdb=" CD  ARG B  73 "
           pdb=" NE  ARG B  73 "
           pdb=" CZ  ARG B  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.96  -50.04     2      1.50e+01 4.44e-03 1.25e+01
  dihedral pdb=" CA  THR D 155 "
           pdb=" C   THR D 155 "
           pdb=" N   PRO D 156 "
           pdb=" CA  PRO D 156 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.31  -17.69     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 5011 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1155
       0.079 -    0.158: 90
       0.158 -    0.237: 3
       0.237 -    0.315: 0
       0.315 -    0.394: 2
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" C5  GA3 B 401 "
            pdb=" C10 GA3 B 401 "
            pdb=" C4  GA3 B 401 "
            pdb=" C6  GA3 B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -3.19    0.39 2.00e-01 2.50e+01 3.89e+00
  chirality pdb=" C9  GA3 B 401 "
            pdb=" C10 GA3 B 401 "
            pdb=" C11 GA3 B 401 "
            pdb=" C8  GA3 B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.24    2.56   -0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" C4  GA3 B 401 "
            pdb=" C19 GA3 B 401 "
            pdb=" C3  GA3 B 401 "
            pdb=" C5  GA3 B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      3.16    2.92    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1247 not shown)

  Planarity restraints: 1440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 155 "   -0.072 5.00e-02 4.00e+02   1.07e-01 1.85e+01
        pdb=" N   PRO D 156 "    0.186 5.00e-02 4.00e+02
        pdb=" CA  PRO D 156 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO D 156 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  43 "    0.050 5.00e-02 4.00e+02   7.59e-02 9.23e+00
        pdb=" N   PRO D  44 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO D  44 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO D  44 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 140 "    0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO D 141 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO D 141 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 141 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1437 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 103
        2.66 -     3.22: 7335
        3.22 -     3.78: 12181
        3.78 -     4.34: 17078
        4.34 -     4.90: 28375
  Nonbonded interactions: 65072
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 470 "
            pdb=" OG  SER A 474 "
     model   vdw
     2.104 3.040
  nonbonded pdb=" OD1 ASP C  48 "
            pdb=" OG1 THR C  51 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O   LEU A 463 "
            pdb=" OG1 THR A 467 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   PHE A 304 "
            pdb=" OG1 THR A 308 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   CYS C  57 "
            pdb=" NH2 ARG D 145 "
     model   vdw
     2.247 3.120
  ... (remaining 65067 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.560
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.070
  Find NCS groups from input model:        0.080
  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:12.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
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      :  0.003   0.054   8256  Z= 0.149
  Angle     :  0.578   8.181  11196  Z= 0.294
  Chirality :  0.044   0.394   1250
  Planarity :  0.005   0.107   1440
  Dihedral  : 18.075  90.060   3100
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.41 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.14 (0.26), residues: 1004
  helix:  0.45 (0.22), residues: 541
  sheet:  0.02 (0.49), residues: 106
  loop : -0.81 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.004   0.001   HIS C  79 
 PHE   0.012   0.001   PHE B 340 
 TYR   0.010   0.001   TYR A 495 
 ARG   0.009   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21237 (  431)
  hydrogen bonds       : angle       6.76002 ( 1317)
  covalent geometry    : bond        0.00346 ( 8256)
  covalent geometry    : angle       0.57785 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.7001 (mtm) cc_final: 0.6752 (mtt)
  outliers start: 24
  outliers final: 19
  residues processed: 126
  average time/residue: 0.9955
  time to fit residues: 134.9129
Evaluate side-chains
  121 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  396 SER
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  171 SER
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain D residue   29 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0370
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0370
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 GLN
A 395 ASN
A 418 ASN
A 487 GLN
A 534 HIS
A 551 ASN
** C  63 HIS ** 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 = 0.4068 r_free = 0.4068 target = 0.170933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.145525 restraints weight = 9973.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.77
r_work: 0.3724 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3626 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.0906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8256  Z= 0.117
  Angle     :  0.538   6.337  11196  Z= 0.281
  Chirality :  0.041   0.197   1250
  Planarity :  0.004   0.054   1440
  Dihedral  :  6.297  42.180   1202
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 22.05 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.48 (0.26), residues: 1004
  helix:  1.08 (0.22), residues: 552
  sheet:  0.23 (0.50), residues: 108
  loop : -0.80 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.005   0.001   HIS A  83 
 PHE   0.009   0.001   PHE A 304 
 TYR   0.017   0.001   TYR A 495 
 ARG   0.007   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04880 (  431)
  hydrogen bonds       : angle       4.53943 ( 1317)
  covalent geometry    : bond        0.00240 ( 8256)
  covalent geometry    : angle       0.53758 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6767 (mm-30)
REVERT: A  565 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7262 (tp)
REVERT: A  566 MET cc_start: 0.8543 (mtt) cc_final: 0.8343 (mtm)
REVERT: B   36 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6074 (mtp180)
REVERT: D  102 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.6857 (pt)
  outliers start: 27
  outliers final: 9
  residues processed: 124
  average time/residue: 1.1628
  time to fit residues: 154.4003
Evaluate side-chains
  115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  155 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0370
   chunk 79 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
A 542 GLN
** C  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.170098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.144611 restraints weight = 10279.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 1.79
r_work: 0.3717 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8256  Z= 0.126
  Angle     :  0.528   6.494  11196  Z= 0.275
  Chirality :  0.041   0.174   1250
  Planarity :  0.004   0.040   1440
  Dihedral  :  5.216  42.129   1180
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.25 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.65 (0.27), residues: 1004
  helix:  1.21 (0.22), residues: 558
  sheet:  0.35 (0.49), residues: 108
  loop : -0.78 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.004   0.001   HIS C  79 
 PHE   0.012   0.001   PHE B 340 
 TYR   0.014   0.001   TYR A 495 
 ARG   0.008   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04515 (  431)
  hydrogen bonds       : angle       4.28791 ( 1317)
  covalent geometry    : bond        0.00287 ( 8256)
  covalent geometry    : angle       0.52791 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6835 (mm-30)
REVERT: B   36 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6278 (mtp180)
REVERT: C  102 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6658 (mpt-90)
REVERT: D  143 GLU cc_start: 0.6766 (mp0) cc_final: 0.6446 (mm-30)
  outliers start: 35
  outliers final: 15
  residues processed: 134
  average time/residue: 1.1467
  time to fit residues: 163.6486
Evaluate side-chains
  117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 68 optimal weight:    0.0370
   chunk 57 optimal weight:    0.3980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.172182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.146996 restraints weight = 10128.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 1.79
r_work: 0.3747 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3648 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8256  Z= 0.099
  Angle     :  0.492   6.157  11196  Z= 0.255
  Chirality :  0.039   0.147   1250
  Planarity :  0.004   0.041   1440
  Dihedral  :  4.763  42.480   1179
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 22.84 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.92 (0.27), residues: 1004
  helix:  1.46 (0.22), residues: 559
  sheet:  0.45 (0.49), residues: 108
  loop : -0.72 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.009   0.001   PHE A 304 
 TYR   0.014   0.001   TYR A 495 
 ARG   0.008   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03659 (  431)
  hydrogen bonds       : angle       4.05005 ( 1317)
  covalent geometry    : bond        0.00215 ( 8256)
  covalent geometry    : angle       0.49200 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.7676 (mp) cc_final: 0.7167 (mp)
REVERT: A  258 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5705 (mmm)
REVERT: A  271 ARG cc_start: 0.7421 (ptm160) cc_final: 0.6804 (ptt180)
REVERT: A  406 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6751 (mm-30)
REVERT: B   36 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.6235 (mtp180)
REVERT: B   95 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.4667 (tt)
REVERT: C  102 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6631 (mpt-90)
REVERT: D  102 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.6916 (mp)
REVERT: D  143 GLU cc_start: 0.6770 (mp0) cc_final: 0.6470 (mm-30)
  outliers start: 24
  outliers final: 12
  residues processed: 125
  average time/residue: 1.1808
  time to fit residues: 157.2732
Evaluate side-chains
  123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0020
   chunk 62 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0770
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.3946

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

Flipped N/Q/H residues before XYZ refinement:
B 332 ASN
** C  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.172938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.147582 restraints weight = 10054.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3826 rms_B_bonded: 1.79
r_work: 0.3756 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8256  Z= 0.096
  Angle     :  0.478   6.036  11196  Z= 0.248
  Chirality :  0.039   0.133   1250
  Planarity :  0.004   0.042   1440
  Dihedral  :  4.557  42.089   1178
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.41 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  1.08 (0.27), residues: 1004
  helix:  1.59 (0.22), residues: 559
  sheet:  0.60 (0.49), residues: 108
  loop : -0.68 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.009   0.001   PHE B 340 
 TYR   0.013   0.001   TYR A 495 
 ARG   0.006   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  431)
  hydrogen bonds       : angle       3.96706 ( 1317)
  covalent geometry    : bond        0.00209 ( 8256)
  covalent geometry    : angle       0.47815 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.7630 (mp) cc_final: 0.7116 (mp)
REVERT: A  258 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5651 (mmm)
REVERT: A  271 ARG cc_start: 0.7385 (ptm160) cc_final: 0.6777 (ptt180)
REVERT: A  406 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6757 (mm-30)
REVERT: B   36 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6255 (mtp180)
REVERT: B   73 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7449 (mpp-170)
REVERT: B   95 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.4643 (tt)
REVERT: C  102 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6637 (mpt-90)
REVERT: D  102 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.6930 (mp)
REVERT: D  143 GLU cc_start: 0.6816 (mp0) cc_final: 0.6486 (mm-30)
  outliers start: 24
  outliers final: 13
  residues processed: 119
  average time/residue: 1.1811
  time to fit residues: 149.8346
Evaluate side-chains
  119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 67 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0000
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 335 GLN
B 214 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.169298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.143786 restraints weight = 10180.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.78
r_work: 0.3709 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3609 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8256  Z= 0.142
  Angle     :  0.537   6.945  11196  Z= 0.278
  Chirality :  0.042   0.129   1250
  Planarity :  0.004   0.039   1440
  Dihedral  :  4.594  19.894   1176
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 21.93 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.78 (0.26), residues: 1004
  helix:  1.31 (0.22), residues: 556
  sheet:  0.64 (0.49), residues: 106
  loop : -0.78 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 174 
 HIS   0.005   0.001   HIS C  79 
 PHE   0.014   0.001   PHE B 340 
 TYR   0.015   0.002   TYR A 495 
 ARG   0.005   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04462 (  431)
  hydrogen bonds       : angle       4.16579 ( 1317)
  covalent geometry    : bond        0.00333 ( 8256)
  covalent geometry    : angle       0.53739 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 105
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.6914 (mtm) cc_final: 0.6704 (mtt)
REVERT: A  211 LEU cc_start: 0.7760 (mp) cc_final: 0.7184 (mp)
REVERT: A  271 ARG cc_start: 0.7425 (ptm160) cc_final: 0.6576 (ptp-170)
REVERT: A  406 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6842 (mm-30)
REVERT: A  513 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8262 (mm-30)
REVERT: B   36 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6452 (mtp180)
REVERT: B   73 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7528 (mpp-170)
REVERT: C  102 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6686 (mpt-90)
REVERT: D  102 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.6977 (mp)
REVERT: D  143 GLU cc_start: 0.6859 (mp0) cc_final: 0.6498 (mm-30)
  outliers start: 39
  outliers final: 20
  residues processed: 131
  average time/residue: 1.0670
  time to fit residues: 149.2535
Evaluate side-chains
  123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 68 optimal weight:    0.3980
   chunk 52 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0000
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
B 332 ASN
C  89 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.170988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.145551 restraints weight = 10116.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 1.78
r_work: 0.3734 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3633 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8256  Z= 0.105
  Angle     :  0.496   6.147  11196  Z= 0.258
  Chirality :  0.040   0.127   1250
  Planarity :  0.004   0.040   1440
  Dihedral  :  4.410  19.430   1176
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 22.95 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.94 (0.27), residues: 1004
  helix:  1.45 (0.22), residues: 559
  sheet:  0.54 (0.49), residues: 108
  loop : -0.69 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.010   0.001   PHE B 340 
 TYR   0.014   0.001   TYR A 495 
 ARG   0.005   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  431)
  hydrogen bonds       : angle       4.04848 ( 1317)
  covalent geometry    : bond        0.00236 ( 8256)
  covalent geometry    : angle       0.49561 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 103
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.7692 (mp) cc_final: 0.7162 (mp)
REVERT: A  271 ARG cc_start: 0.7322 (ptm160) cc_final: 0.6520 (ptp-170)
REVERT: A  406 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6845 (mm-30)
REVERT: A  491 MET cc_start: 0.7717 (mmm) cc_final: 0.7472 (mmp)
REVERT: A  518 LEU cc_start: 0.7529 (tp) cc_final: 0.7278 (tp)
REVERT: B   36 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6363 (mtp180)
REVERT: B   73 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7494 (mpp-170)
REVERT: B   95 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.4603 (tt)
REVERT: C  102 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6665 (mpt-90)
REVERT: D  102 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.6965 (mp)
REVERT: D  143 GLU cc_start: 0.6828 (mp0) cc_final: 0.6477 (mm-30)
  outliers start: 32
  outliers final: 19
  residues processed: 121
  average time/residue: 1.1194
  time to fit residues: 144.7520
Evaluate side-chains
  127 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0050
   chunk 97 optimal weight:    0.6980
   chunk 71 optimal weight:    0.3980
   chunk 91 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
B 332 ASN
** C  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.171519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.146044 restraints weight = 10166.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 1.79
r_work: 0.3737 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8256  Z= 0.103
  Angle     :  0.490   6.158  11196  Z= 0.254
  Chirality :  0.040   0.219   1250
  Planarity :  0.004   0.041   1440
  Dihedral  :  4.326  18.879   1176
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 23.75 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.99 (0.27), residues: 1004
  helix:  1.50 (0.22), residues: 560
  sheet:  0.60 (0.49), residues: 108
  loop : -0.72 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 246 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.010   0.001   PHE B 340 
 TYR   0.013   0.001   TYR A 495 
 ARG   0.005   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (  431)
  hydrogen bonds       : angle       3.99360 ( 1317)
  covalent geometry    : bond        0.00232 ( 8256)
  covalent geometry    : angle       0.48958 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.7669 (mp) cc_final: 0.7109 (mp)
REVERT: A  258 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5711 (mmm)
REVERT: A  271 ARG cc_start: 0.7370 (ptm160) cc_final: 0.6517 (ptp-170)
REVERT: A  406 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6812 (mm-30)
REVERT: A  518 LEU cc_start: 0.7510 (tp) cc_final: 0.7277 (tp)
REVERT: B   36 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6302 (mtp180)
REVERT: B   95 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.4592 (tt)
REVERT: C  102 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6656 (mpt-90)
REVERT: D  102 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.6960 (mp)
REVERT: D  143 GLU cc_start: 0.6808 (mp0) cc_final: 0.6473 (mm-30)
  outliers start: 28
  outliers final: 18
  residues processed: 120
  average time/residue: 1.1774
  time to fit residues: 151.4001
Evaluate side-chains
  126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0040
   chunk 75 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 63 optimal weight:    0.2980
   chunk 78 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
B 332 ASN
** C  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.172364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.146924 restraints weight = 10311.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 1.81
r_work: 0.3744 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8256  Z= 0.101
  Angle     :  0.486   5.984  11196  Z= 0.253
  Chirality :  0.040   0.170   1250
  Planarity :  0.004   0.041   1440
  Dihedral  :  4.249  18.341   1176
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.98 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  1.07 (0.27), residues: 1004
  helix:  1.57 (0.22), residues: 560
  sheet:  0.64 (0.49), residues: 108
  loop : -0.70 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 246 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.010   0.001   PHE B 340 
 TYR   0.013   0.001   TYR A 495 
 ARG   0.004   0.000   ARG C 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  431)
  hydrogen bonds       : angle       3.96344 ( 1317)
  covalent geometry    : bond        0.00226 ( 8256)
  covalent geometry    : angle       0.48585 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.6744 (mtm) cc_final: 0.6532 (mtt)
REVERT: A  211 LEU cc_start: 0.7648 (mp) cc_final: 0.7070 (mp)
REVERT: A  258 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5730 (mmm)
REVERT: A  271 ARG cc_start: 0.7331 (ptm160) cc_final: 0.6504 (ptp-170)
REVERT: A  406 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6816 (mm-30)
REVERT: A  518 LEU cc_start: 0.7550 (tp) cc_final: 0.7316 (tp)
REVERT: B   36 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6263 (mtp180)
REVERT: B   95 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.4578 (tt)
REVERT: C  102 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6627 (mpt-90)
REVERT: D  102 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.6928 (mp)
REVERT: D  143 GLU cc_start: 0.6779 (mp0) cc_final: 0.6452 (mm-30)
  outliers start: 29
  outliers final: 20
  residues processed: 122
  average time/residue: 1.1794
  time to fit residues: 153.2976
Evaluate side-chains
  128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    0.0870
   chunk 8 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 72 optimal weight:    0.2980
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0770
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 214 ASN
B 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.172646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.147345 restraints weight = 10095.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 1.78
r_work: 0.3750 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8256  Z= 0.098
  Angle     :  0.479   5.970  11196  Z= 0.250
  Chirality :  0.040   0.147   1250
  Planarity :  0.004   0.042   1440
  Dihedral  :  4.205  18.110   1176
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 24.43 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  1.14 (0.27), residues: 1004
  helix:  1.63 (0.22), residues: 560
  sheet:  0.71 (0.49), residues: 108
  loop : -0.68 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 246 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.010   0.001   PHE B 340 
 TYR   0.012   0.001   TYR A 495 
 ARG   0.007   0.000   ARG C 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03549 (  431)
  hydrogen bonds       : angle       3.92441 ( 1317)
  covalent geometry    : bond        0.00218 ( 8256)
  covalent geometry    : angle       0.47927 (11196)

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.6837 (mtm) cc_final: 0.6619 (mtt)
REVERT: A  211 LEU cc_start: 0.7641 (mp) cc_final: 0.7095 (mp)
REVERT: A  258 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5730 (mmm)
REVERT: A  271 ARG cc_start: 0.7280 (ptm160) cc_final: 0.6488 (ptp-170)
REVERT: A  406 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6810 (mm-30)
REVERT: A  518 LEU cc_start: 0.7546 (tp) cc_final: 0.7313 (tp)
REVERT: B   36 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6279 (mtp180)
REVERT: B   95 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.4557 (tt)
REVERT: C  102 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6615 (mpt-90)
REVERT: D  102 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.6923 (mp)
REVERT: D  143 GLU cc_start: 0.6705 (mp0) cc_final: 0.6390 (mm-30)
  outliers start: 27
  outliers final: 17
  residues processed: 121
  average time/residue: 1.1619
  time to fit residues: 149.5862
Evaluate side-chains
  125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  347 GLU
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  576 THR
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  104 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    0.0020
   chunk 88 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0970
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 214 ASN
B 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.172864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.147436 restraints weight = 10224.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 1.80
r_work: 0.3751 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8256  Z= 0.100
  Angle     :  0.487   5.978  11196  Z= 0.254
  Chirality :  0.040   0.133   1250
  Planarity :  0.004   0.041   1440
  Dihedral  :  4.160  17.762   1176
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 24.77 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  1.17 (0.27), residues: 1004
  helix:  1.66 (0.22), residues: 560
  sheet:  0.74 (0.49), residues: 108
  loop : -0.68 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 246 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.010   0.001   PHE B 340 
 TYR   0.012   0.001   TYR A 495 
 ARG   0.007   0.000   ARG C 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03526 (  431)
  hydrogen bonds       : angle       3.91779 ( 1317)
  covalent geometry    : bond        0.00224 ( 8256)
  covalent geometry    : angle       0.48651 (11196)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6149.15 seconds
wall clock time: 106 minutes 5.71 seconds (6365.71 seconds total)