Starting phenix.real_space_refine
on Wed Mar 12 19:13:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dsn_30839/03_2025/7dsn_30839_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dsn_30839/03_2025/7dsn_30839.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dsn_30839/03_2025/7dsn_30839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dsn_30839/03_2025/7dsn_30839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dsn_30839/03_2025/7dsn_30839_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dsn_30839/03_2025/7dsn_30839_neut.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      27      5.16       5
     C    4939      2.51       5
     N    1192      2.21       5
     O    1375      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7534
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3670
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 22, 'TRANS': 448}
    Chain: "B"
      Number of atoms: 3586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3586
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 24, 'TRANS': 439}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'3PH': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 118
          Unusual residues: {'HO9': 1, 'Y01': 2}
          Classifications: {'undetermined': 3, 'water': 17}
          Link IDs: {None: 19}
  Time building chain proxies: 5.15, per 1000 atoms: 0.68
  Number of scatterers: 7534
  At special positions: 0
  Unit cell: (83.699, 86.96, 126.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       1     15.00
     O    1375      8.00
     N    1192      7.00
     C    4939      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " distance=2.19

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 6 sheets defined
      55.6% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 178 through 207
      removed outlier: 3.671A  pdb=" N   ARG A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.778A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
      removed outlier: 3.799A  pdb=" N   LYS A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 249
      No H-bonds generated for 'chain 'A' and resid 247 through 249'
    Processing helix  chain 'A' and resid 250 through 255
    Processing helix  chain 'A' and resid 287 through 300
      removed outlier: 3.821A  pdb=" N   SER A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS A 300 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 342
      removed outlier: 3.725A  pdb=" N   VAL A 331 " --> pdb=" O   VAL A 327 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 3.751A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.698A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 427
      removed outlier: 3.670A  pdb=" N   THR A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
      removed outlier: 3.621A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 459
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 520 through 532
      removed outlier: 3.558A  pdb=" N   ARG A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 539
    Processing helix  chain 'B' and resid 51 through 64
      removed outlier: 3.563A  pdb=" N   GLY B  55 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 78
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.681A  pdb=" N   LEU B  86 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 125
      removed outlier: 3.632A  pdb=" N   GLY B 125 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 139
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.681A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL B 174 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B 180 " --> pdb=" O   CYS B 176 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 220
      removed outlier: 3.932A  pdb=" N   ALA B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN B 197 " --> pdb=" O   ALA B 193 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU B 210 " --> pdb=" O   LEU B 206 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 248
      removed outlier: 3.609A  pdb=" N   ALA B 246 " --> pdb=" O   ASN B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 263
    Processing helix  chain 'B' and resid 269 through 274
    Processing helix  chain 'B' and resid 274 through 300
      Proline residue:  B 283  - end of helix
      removed outlier: 3.624A  pdb=" N   LEU B 287 " --> pdb=" O   PRO B 283 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL B 290 " --> pdb=" O   THR B 286 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA B 295 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 3.651A  pdb=" N   LEU B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 325 through 333
      removed outlier: 3.504A  pdb=" N   VAL B 329 " --> pdb=" O   TRP B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 356
      removed outlier: 3.606A  pdb=" N   ASN B 340 " --> pdb=" O   PHE B 336 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY B 341 " --> pdb=" O   GLY B 337 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER B 342 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR B 345 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER B 347 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU B 356 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
      removed outlier: 3.583A  pdb=" N   PHE B 379 " --> pdb=" O   PRO B 375 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   THR B 384 " --> pdb=" O   THR B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 390
      removed outlier: 3.610A  pdb=" N   SER B 390 " --> pdb=" O   TYR B 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 387 through 390'
    Processing helix  chain 'B' and resid 393 through 397
      removed outlier: 3.834A  pdb=" N   ILE B 397 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 420
      removed outlier: 4.098A  pdb=" N   VAL B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 448
      removed outlier: 3.584A  pdb=" N   LEU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 453
      removed outlier: 3.567A  pdb=" N   LYS B 453 " --> pdb=" O   VAL B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 476
      removed outlier: 3.530A  pdb=" N   THR B 463 " --> pdb=" O   GLY B 459 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ILE B 465 " --> pdb=" O   GLY B 461 " (cutoff:3.500A)
      Proline residue:  B 470  - end of helix
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.860A  pdb=" N   GLN B 487 " --> pdb=" O   LYS B 483 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402
      removed outlier: 6.548A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 8.301A  pdb=" N   GLY A 380 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL A 348 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLY A 345 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU A 262 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.547A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594
    Processing sheet with id=AA6, first strand: chain 'B' and resid 365 through 366

    334 hydrogen bonds defined for protein.
    972 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: 2.15

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1168
        1.31 -     1.43: 2050
        1.43 -     1.56: 4424
        1.56 -     1.68: 25
        1.68 -     1.81: 40
  Bond restraints: 7707
  Sorted by residual:
  bond pdb=" CAI Y01 B 603 "
       pdb=" CAZ Y01 B 603 "
    ideal  model  delta    sigma   weight residual
    1.332  1.555 -0.223 2.00e-02 2.50e+03 1.24e+02
  bond pdb=" CAI Y01 B 602 "
       pdb=" CAZ Y01 B 602 "
    ideal  model  delta    sigma   weight residual
    1.332  1.554 -0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" C22 HO9 B 601 "
       pdb=" C25 HO9 B 601 "
    ideal  model  delta    sigma   weight residual
    1.380  1.564 -0.184 2.00e-02 2.50e+03 8.46e+01
  bond pdb=" C23 HO9 B 601 "
       pdb=" C28 HO9 B 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.565 -0.175 2.00e-02 2.50e+03 7.68e+01
  bond pdb=" CBG Y01 B 602 "
       pdb=" CBI Y01 B 602 "
    ideal  model  delta    sigma   weight residual
    1.537  1.385  0.152 2.00e-02 2.50e+03 5.78e+01
  ... (remaining 7702 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 10135
        2.66 -     5.32: 287
        5.32 -     7.98: 58
        7.98 -    10.64: 14
       10.64 -    13.30: 3
  Bond angle restraints: 10497
  Sorted by residual:
  angle pdb=" N   VAL B 396 "
        pdb=" CA  VAL B 396 "
        pdb=" C   VAL B 396 "
      ideal   model   delta    sigma   weight residual
     112.83  106.26    6.57 9.90e-01 1.02e+00 4.40e+01
  angle pdb=" C   PRO A 209 "
        pdb=" N   ARG A 210 "
        pdb=" CA  ARG A 210 "
      ideal   model   delta    sigma   weight residual
     121.54  131.91  -10.37 1.91e+00 2.74e-01 2.95e+01
  angle pdb=" N   ILE B  68 "
        pdb=" CA  ILE B  68 "
        pdb=" C   ILE B  68 "
      ideal   model   delta    sigma   weight residual
     112.83  107.51    5.32 9.90e-01 1.02e+00 2.89e+01
  angle pdb=" N   THR A 163 "
        pdb=" CA  THR A 163 "
        pdb=" C   THR A 163 "
      ideal   model   delta    sigma   weight residual
     111.71  105.32    6.39 1.34e+00 5.57e-01 2.27e+01
  angle pdb=" C   THR B  71 "
        pdb=" N   PRO B  72 "
        pdb=" CA  PRO B  72 "
      ideal   model   delta    sigma   weight residual
     119.84  114.06    5.78 1.25e+00 6.40e-01 2.14e+01
  ... (remaining 10492 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.07: 4553
       35.07 -    70.15: 126
       70.15 -   105.22: 20
      105.22 -   140.29: 31
      140.29 -   175.37: 7
  Dihedral angle restraints: 4737
    sinusoidal: 2057
      harmonic: 2680
  Sorted by residual:
  dihedral pdb=" CA  GLY A 410 "
           pdb=" C   GLY A 410 "
           pdb=" N   SER A 411 "
           pdb=" CA  SER A 411 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.75  -25.25     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  THR B 264 "
           pdb=" C   THR B 264 "
           pdb=" N   GLU B 265 "
           pdb=" CA  GLU B 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.82  -24.18     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  ARG A 210 "
           pdb=" C   ARG A 210 "
           pdb=" N   CYS A 211 "
           pdb=" CA  CYS A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.52   23.48     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 4734 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.192: 1223
       1.192 -    2.383: 0
       2.383 -    3.575: 0
       3.575 -    4.766: 0
       4.766 -    5.958: 10
  Chirality restraints: 1233
  Sorted by residual:
  chirality pdb=" CBI Y01 B 602 "
            pdb=" CAU Y01 B 602 "
            pdb=" CBE Y01 B 602 "
            pdb=" CBG Y01 B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94   -3.02    5.96 2.00e-01 2.50e+01 8.87e+02
  chirality pdb=" CBI Y01 B 603 "
            pdb=" CAU Y01 B 603 "
            pdb=" CBE Y01 B 603 "
            pdb=" CBG Y01 B 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94   -3.00    5.94 2.00e-01 2.50e+01 8.82e+02
  chirality pdb=" CBH Y01 B 602 "
            pdb=" CAT Y01 B 602 "
            pdb=" CAZ Y01 B 602 "
            pdb=" CBF Y01 B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85    2.64   -5.50 2.00e-01 2.50e+01 7.56e+02
  ... (remaining 1230 not shown)

  Planarity restraints: 1286
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 164 "   -0.073 5.00e-02 4.00e+02   1.13e-01 2.04e+01
        pdb=" N   PRO B 165 "    0.195 5.00e-02 4.00e+02
        pdb=" CA  PRO B 165 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO B 165 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 618 "   -0.052 5.00e-02 4.00e+02   7.76e-02 9.63e+00
        pdb=" N   PRO A 619 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 619 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 619 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 282 "   -0.038 5.00e-02 4.00e+02   5.69e-02 5.18e+00
        pdb=" N   PRO B 283 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 283 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 283 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1283 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 199
        2.69 -     3.24: 6731
        3.24 -     3.79: 11474
        3.79 -     4.35: 15599
        4.35 -     4.90: 25421
  Nonbonded interactions: 59424
  Sorted by model distance:
  nonbonded pdb=" O   VAL B  70 "
            pdb=" OG1 THR B  71 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" OG  SER A 407 "
            pdb=" O   LEU A 436 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" CG2 ILE B 397 "
            pdb=" O21 HO9 B 601 "
     model   vdw
     2.254 3.460
  nonbonded pdb=" CG2 ILE B 147 "
            pdb=" C27 HO9 B 601 "
     model   vdw
     2.265 3.760
  nonbonded pdb=" OG  SER B 113 "
            pdb=" O   THR B 264 "
     model   vdw
     2.271 3.040
  ... (remaining 59419 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.670
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
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      :  0.012   0.223   7707  Z= 0.706
  Angle     :  1.143  13.297  10497  Z= 0.597
  Chirality :  0.490   5.958   1233
  Planarity :  0.008   0.113   1282
  Dihedral  : 22.156 175.366   3012
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  :  6.66 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  5.70 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.42 (0.21), residues: 931
  helix: -2.79 (0.17), residues: 486
  sheet: -1.73 (0.59), residues: 63
  loop : -3.19 (0.25), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 220 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.022   0.002   PHE A 497 
 TYR   0.022   0.002   TYR B 103 
 ARG   0.005   0.001   ARG A 556 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.812 
Fit side-chains
REVERT: B   51 THR cc_start: 0.8410 (m) cc_final: 0.8194 (m)
REVERT: B  195 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7056 (mtm180)
REVERT: B  365 MET cc_start: 0.8597 (mtt) cc_final: 0.8290 (mtt)
REVERT: B  401 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.7022 (p)
REVERT: B  438 PHE cc_start: 0.7291 (t80) cc_final: 0.7078 (t80)
REVERT: B  496 CYS cc_start: 0.7983 (m) cc_final: 0.7733 (m)
REVERT: B  500 MET cc_start: 0.8380 (mtt) cc_final: 0.8051 (mtm)
  outliers start: 12
  outliers final: 5
  residues processed: 155
  average time/residue: 0.2208
  time to fit residues: 45.3518
Evaluate side-chains
  115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  164 CYS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  505 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0060
   chunk 54 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
A 353 ASN
A 483 GLN
A 539 HIS
B  47 GLN
B 261 ASN
B 304 GLN
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 420 HIS
B 501 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.153727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.114401 restraints weight = 9542.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.80
r_work: 0.2959 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7707  Z= 0.194
  Angle     :  1.244  32.694  10497  Z= 0.485
  Chirality :  0.107   1.792   1233
  Planarity :  0.005   0.057   1282
  Dihedral  : 23.055 178.875   1376
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.23 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.90 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.25), residues: 931
  helix: -1.24 (0.21), residues: 494
  sheet: -1.05 (0.63), residues: 63
  loop : -2.90 (0.27), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 477 
 HIS   0.011   0.001   HIS B 420 
 PHE   0.021   0.001   PHE B 379 
 TYR   0.010   0.002   TYR A 554 
 ARG   0.005   0.001   ARG A 440 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.854 
Fit side-chains
REVERT: B   51 THR cc_start: 0.7956 (m) cc_final: 0.7702 (m)
REVERT: B   78 GLU cc_start: 0.7110 (mp0) cc_final: 0.6861 (mp0)
REVERT: B  195 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7435 (mtm180)
REVERT: B  271 TYR cc_start: 0.8879 (m-80) cc_final: 0.8517 (m-80)
REVERT: B  433 LEU cc_start: 0.7075 (tp) cc_final: 0.6860 (tp)
REVERT: B  438 PHE cc_start: 0.7596 (t80) cc_final: 0.7368 (t80)
REVERT: B  500 MET cc_start: 0.8108 (mtt) cc_final: 0.7868 (mtm)
  outliers start: 14
  outliers final: 8
  residues processed: 122
  average time/residue: 0.2272
  time to fit residues: 38.2384
Evaluate side-chains
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  572 ASP
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  267 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 91 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
B 304 GLN
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.154683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.117093 restraints weight = 9686.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.81
r_work: 0.3004 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7707  Z= 0.205
  Angle     :  1.204  32.649  10497  Z= 0.463
  Chirality :  0.109   1.866   1233
  Planarity :  0.005   0.052   1282
  Dihedral  : 22.894 177.887   1366
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.34 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.53 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.95 (0.26), residues: 931
  helix: -0.40 (0.23), residues: 489
  sheet: -0.71 (0.63), residues: 64
  loop : -2.60 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 477 
 HIS   0.002   0.001   HIS B 367 
 PHE   0.018   0.001   PHE B 474 
 TYR   0.011   0.002   TYR A 226 
 ARG   0.004   0.000   ARG A 440 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.761 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 LEU cc_start: 0.9030 (tp) cc_final: 0.8802 (tp)
REVERT: A  593 LYS cc_start: 0.8012 (pptt) cc_final: 0.7403 (mtpt)
REVERT: B   51 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7657 (m)
REVERT: B  195 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7352 (mtm180)
REVERT: B  271 TYR cc_start: 0.8840 (m-80) cc_final: 0.8532 (m-80)
REVERT: B  319 HIS cc_start: 0.8596 (m-70) cc_final: 0.8378 (m-70)
REVERT: B  433 LEU cc_start: 0.7123 (tp) cc_final: 0.6873 (tp)
REVERT: B  438 PHE cc_start: 0.7553 (t80) cc_final: 0.7333 (t80)
REVERT: B  500 MET cc_start: 0.8120 (mtt) cc_final: 0.7907 (mtm)
  outliers start: 20
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1976
  time to fit residues: 34.0257
Evaluate side-chains
  113 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  263 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0970
   chunk 72 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 221 HIS
A 296 GLN
B 304 GLN
B 367 HIS
B 501 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.153357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.116220 restraints weight = 9577.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.71
r_work: 0.2988 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7707  Z= 0.186
  Angle     :  1.187  32.899  10497  Z= 0.451
  Chirality :  0.108   1.827   1233
  Planarity :  0.004   0.049   1282
  Dihedral  : 22.849 174.926   1366
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.91 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.31 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.41 (0.27), residues: 931
  helix:  0.06 (0.23), residues: 498
  sheet: -0.74 (0.61), residues: 67
  loop : -2.38 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 477 
 HIS   0.002   0.001   HIS A 557 
 PHE   0.014   0.001   PHE B 351 
 TYR   0.011   0.001   TYR A 226 
 ARG   0.004   0.000   ARG A 430 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
REVERT: A  593 LYS cc_start: 0.7977 (pptt) cc_final: 0.7401 (mtpt)
REVERT: B   51 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7623 (m)
REVERT: B  195 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7416 (mtm180)
REVERT: B  271 TYR cc_start: 0.8842 (m-80) cc_final: 0.8578 (m-80)
REVERT: B  319 HIS cc_start: 0.8596 (m-70) cc_final: 0.8325 (m-70)
REVERT: B  365 MET cc_start: 0.8880 (mtt) cc_final: 0.8360 (mtt)
REVERT: B  401 SER cc_start: 0.6856 (m) cc_final: 0.6283 (p)
REVERT: B  438 PHE cc_start: 0.7474 (t80) cc_final: 0.7264 (t80)
  outliers start: 24
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1919
  time to fit residues: 32.4134
Evaluate side-chains
  117 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  267 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0000
   chunk 90 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 16 optimal weight:    0.4980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 296 GLN
B 304 GLN
B 501 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.154740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.118293 restraints weight = 9487.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.69
r_work: 0.3026 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7707  Z= 0.189
  Angle     :  1.194  32.902  10497  Z= 0.453
  Chirality :  0.108   1.821   1233
  Planarity :  0.004   0.048   1282
  Dihedral  : 22.831 177.335   1366
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.12 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 13.94 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.10 (0.27), residues: 931
  helix:  0.35 (0.23), residues: 498
  sheet: -0.67 (0.61), residues: 67
  loop : -2.28 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.015   0.001   PHE B 351 
 TYR   0.010   0.001   TYR A 226 
 ARG   0.003   0.000   ARG A 440 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A  593 LYS cc_start: 0.7974 (pptt) cc_final: 0.7417 (mtpt)
REVERT: B   51 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7620 (m)
REVERT: B  271 TYR cc_start: 0.8834 (m-80) cc_final: 0.8578 (m-80)
REVERT: B  319 HIS cc_start: 0.8581 (m-70) cc_final: 0.8347 (m-70)
REVERT: B  401 SER cc_start: 0.6880 (m) cc_final: 0.6346 (p)
REVERT: B  438 PHE cc_start: 0.7483 (t80) cc_final: 0.7264 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1650
  time to fit residues: 27.7427
Evaluate side-chains
  123 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  248 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 85 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 78 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
B 501 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.155753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.119475 restraints weight = 9521.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.66
r_work: 0.2995 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7707  Z= 0.197
  Angle     :  1.183  32.786  10497  Z= 0.449
  Chirality :  0.108   1.813   1233
  Planarity :  0.004   0.047   1282
  Dihedral  : 22.831 176.479   1366
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.12 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 14.96 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.83 (0.28), residues: 931
  helix:  0.61 (0.24), residues: 498
  sheet: -0.66 (0.61), residues: 67
  loop : -2.19 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 474 
 TYR   0.011   0.001   TYR A 226 
 ARG   0.002   0.000   ARG A 440 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A  593 LYS cc_start: 0.7983 (pptt) cc_final: 0.7405 (mtpt)
REVERT: B   51 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7593 (m)
REVERT: B  271 TYR cc_start: 0.8829 (m-80) cc_final: 0.8610 (m-80)
REVERT: B  319 HIS cc_start: 0.8563 (m-70) cc_final: 0.8286 (m-70)
REVERT: B  365 MET cc_start: 0.8869 (mtt) cc_final: 0.8288 (mtt)
REVERT: B  401 SER cc_start: 0.6809 (m) cc_final: 0.6310 (p)
REVERT: B  438 PHE cc_start: 0.7437 (t80) cc_final: 0.7199 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1686
  time to fit residues: 29.0135
Evaluate side-chains
  124 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  449 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.150788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.113441 restraints weight = 9610.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.68
r_work: 0.2969 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7707  Z= 0.288
  Angle     :  1.221  32.790  10497  Z= 0.471
  Chirality :  0.109   1.795   1233
  Planarity :  0.004   0.048   1282
  Dihedral  : 22.881 177.366   1366
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.87 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.72 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.80 (0.28), residues: 931
  helix:  0.63 (0.24), residues: 495
  sheet: -0.58 (0.60), residues: 67
  loop : -2.17 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.019   0.001   PHE B 351 
 TYR   0.014   0.002   TYR A 226 
 ARG   0.007   0.000   ARG A 440 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7264 (tptp)
REVERT: A  593 LYS cc_start: 0.7986 (pptt) cc_final: 0.7420 (mtpt)
REVERT: B   51 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7778 (m)
REVERT: B  271 TYR cc_start: 0.8881 (m-80) cc_final: 0.8603 (m-80)
REVERT: B  401 SER cc_start: 0.6816 (m) cc_final: 0.6378 (p)
REVERT: B  438 PHE cc_start: 0.7520 (t80) cc_final: 0.7308 (t80)
REVERT: B  478 TRP cc_start: 0.8234 (t60) cc_final: 0.8029 (t-100)
  outliers start: 21
  outliers final: 16
  residues processed: 122
  average time/residue: 0.1666
  time to fit residues: 28.9634
Evaluate side-chains
  121 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  449 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 347 GLN
B 304 GLN
B 501 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.156443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.120197 restraints weight = 9537.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.70
r_work: 0.2994 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7707  Z= 0.198
  Angle     :  1.191  32.598  10497  Z= 0.453
  Chirality :  0.109   1.808   1233
  Planarity :  0.004   0.047   1282
  Dihedral  : 22.792 176.886   1366
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.55 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.10 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.58 (0.28), residues: 931
  helix:  0.83 (0.24), residues: 495
  sheet: -0.47 (0.60), residues: 67
  loop : -2.10 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.021   0.001   PHE B 474 
 TYR   0.011   0.001   TYR A 226 
 ARG   0.005   0.000   ARG A 440 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7185 (tptp)
REVERT: A  593 LYS cc_start: 0.7984 (pptt) cc_final: 0.7394 (mtpt)
REVERT: B   51 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7506 (m)
REVERT: B  271 TYR cc_start: 0.8862 (m-80) cc_final: 0.8615 (m-80)
REVERT: B  401 SER cc_start: 0.6802 (m) cc_final: 0.6387 (p)
REVERT: B  438 PHE cc_start: 0.7513 (t80) cc_final: 0.7301 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 117
  average time/residue: 0.1589
  time to fit residues: 26.9081
Evaluate side-chains
  116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  164 CYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  396 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
B 501 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.157841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.121937 restraints weight = 9478.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.67
r_work: 0.2998 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7707  Z= 0.204
  Angle     :  1.196  32.430  10497  Z= 0.454
  Chirality :  0.109   1.810   1233
  Planarity :  0.004   0.046   1282
  Dihedral  : 22.750 177.166   1366
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.44 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.97 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.50 (0.28), residues: 931
  helix:  0.88 (0.24), residues: 495
  sheet: -0.44 (0.60), residues: 67
  loop : -2.03 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.017   0.001   PHE B 351 
 TYR   0.012   0.001   TYR A 226 
 ARG   0.006   0.000   ARG A 440 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7222 (tptp)
REVERT: A  593 LYS cc_start: 0.7971 (pptt) cc_final: 0.7390 (mtpt)
REVERT: B   51 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7508 (m)
REVERT: B  271 TYR cc_start: 0.8852 (m-80) cc_final: 0.8611 (m-80)
REVERT: B  401 SER cc_start: 0.6714 (m) cc_final: 0.6320 (p)
REVERT: B  438 PHE cc_start: 0.7511 (t80) cc_final: 0.7304 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1750
  time to fit residues: 28.2625
Evaluate side-chains
  114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  164 CYS
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  449 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0770
   chunk 57 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0070
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
B 304 GLN
B 501 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.160273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.124317 restraints weight = 9474.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.66
r_work: 0.3035 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7707  Z= 0.164
  Angle     :  1.184  32.242  10497  Z= 0.448
  Chirality :  0.109   1.820   1233
  Planarity :  0.004   0.046   1282
  Dihedral  : 22.681 178.372   1366
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.77 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.98 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.35 (0.28), residues: 931
  helix:  1.02 (0.24), residues: 494
  sheet: -0.45 (0.61), residues: 67
  loop : -1.96 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 477 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B 474 
 TYR   0.008   0.001   TYR A 226 
 ARG   0.006   0.000   ARG A 440 

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

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

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1862 Ramachandran restraints generated.
    931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 LEU cc_start: 0.8560 (mt) cc_final: 0.8337 (mt)
REVERT: A  593 LYS cc_start: 0.7955 (pptt) cc_final: 0.7396 (mtpt)
REVERT: B   51 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7472 (m)
REVERT: B  304 GLN cc_start: 0.7170 (pt0) cc_final: 0.6612 (pm20)
REVERT: B  433 LEU cc_start: 0.6677 (tp) cc_final: 0.6344 (tp)
REVERT: B  438 PHE cc_start: 0.7493 (t80) cc_final: 0.7290 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 114
  average time/residue: 0.1751
  time to fit residues: 28.1911
Evaluate side-chains
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  449 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0030
   chunk 44 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0050
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4804

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

Flipped N/Q/H residues before XYZ refinement:
B 501 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.157803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.121390 restraints weight = 9481.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.72
r_work: 0.3026 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7707  Z= 0.165
  Angle     :  1.187  32.049  10497  Z= 0.448
  Chirality :  0.109   1.824   1233
  Planarity :  0.004   0.046   1282
  Dihedral  : 22.628 178.830   1366
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.91 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.87 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.28 (0.28), residues: 931
  helix:  1.02 (0.24), residues: 499
  sheet: -0.43 (0.61), residues: 67
  loop : -1.89 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 477 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.017   0.001   PHE B 351 
 TYR   0.009   0.001   TYR A 226 
 ARG   0.006   0.000   ARG A 440 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3835.92 seconds
wall clock time: 67 minutes 47.09 seconds (4067.09 seconds total)