Starting phenix.real_space_refine
on Tue Jan 14 11:13:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yft_39229/01_2025/8yft_39229.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yft_39229/01_2025/8yft_39229.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yft_39229/01_2025/8yft_39229.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yft_39229/01_2025/8yft_39229.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yft_39229/01_2025/8yft_39229.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yft_39229/01_2025/8yft_39229.cif"
  }
  resolution = 3.16
  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=  -0.002 sd=   0.010
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
     Zn      1      6.06       5
     S      36      5.16       5
     C    4164      2.51       5
     N    1065      2.21       5
     O    1242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6508
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4840
          Classifications: {'peptide': 589}
          Link IDs: {'PTRANS': 27, 'TRANS': 561}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1541
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    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: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' ZN': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.51, per 1000 atoms: 1.00
  Number of scatterers: 6508
  At special positions: 0
  Unit cell: (97.98, 74.52, 120.06, 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)
     Zn      1     29.99
     S      36     16.00
     O    1242      8.00
     N    1065      7.00
     C    4164      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.06

  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 A 702 " - " ASN A  53 "
      " NAG C   1 " - " ASN A 216 "
      " NAG D   1 " - " ASN A 322 "
      " NAG E   1 " - " ASN A 299 "
      " NAG F   1 " - " ASN B 343 "
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 882.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 378 "


  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1476

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      54.8% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 54
      removed outlier: 4.161A  pdb=" N   TYR A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   GLU A  38 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 80
      removed outlier: 3.909A  pdb=" N   LYS A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 90 through 103
      removed outlier: 3.665A  pdb=" N   LYS A  94 " --> pdb=" O   ASP A  90 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   SER A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.699A  pdb=" N   GLN A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   TYR A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 154
      removed outlier: 3.713A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   MET A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.517A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLU A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU A 176 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.608A  pdb=" N   GLU A 181 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TYR A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL A 184 " --> pdb=" O   TYR A 180 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 218 through 230
      removed outlier: 4.049A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ASP A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 248
      removed outlier: 4.044A  pdb=" N   VAL A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ARG A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.962A  pdb=" N   TYR A 279 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.856A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 4.390A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 3.846A  pdb=" N   LEU A 370 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A 371 " --> pdb=" O   ASP A 367 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   HIS A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 3.921A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ILE A 407 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.661A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.952A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 534
      removed outlier: 3.627A  pdb=" N   THR A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 549 through 559
      removed outlier: 3.845A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.907A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.841A  pdb=" N   GLU A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLN A 598 " --> pdb=" O   TRP A 594 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ASN A 599 " --> pdb=" O   LEU A 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 4.290A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 387
      removed outlier: 3.848A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 417 through 422
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.134A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 359
      removed outlier: 4.119A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474

    257 hydrogen bonds defined for protein.
    732 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: 1.68

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2055
        1.34 -     1.46: 1751
        1.46 -     1.58: 2830
        1.58 -     1.70: 0
        1.70 -     1.82: 57
  Bond restraints: 6693
  Sorted by residual:
  bond pdb=" CA  TYR A 243 "
       pdb=" C   TYR A 243 "
    ideal  model  delta    sigma   weight residual
    1.524  1.457  0.068 1.28e-02 6.10e+03 2.80e+01
  bond pdb=" N   PHE B 486 "
       pdb=" CA  PHE B 486 "
    ideal  model  delta    sigma   weight residual
    1.453  1.494 -0.041 1.31e-02 5.83e+03 9.58e+00
  bond pdb=" N   ARG B 346 "
       pdb=" CA  ARG B 346 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.23e-02 6.61e+03 8.56e+00
  bond pdb=" N   ASN B 487 "
       pdb=" CA  ASN B 487 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.50e+00
  bond pdb=" N   CYS B 488 "
       pdb=" CA  CYS B 488 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.25e-02 6.40e+03 7.16e+00
  ... (remaining 6688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 8862
        1.83 -     3.66: 196
        3.66 -     5.49: 31
        5.49 -     7.32: 4
        7.32 -     9.15: 3
  Bond angle restraints: 9096
  Sorted by residual:
  angle pdb=" N   PHE B 486 "
        pdb=" CA  PHE B 486 "
        pdb=" CB  PHE B 486 "
      ideal   model   delta    sigma   weight residual
     110.45  119.60   -9.15 1.52e+00 4.33e-01 3.62e+01
  angle pdb=" C   TYR A 243 "
        pdb=" CA  TYR A 243 "
        pdb=" CB  TYR A 243 "
      ideal   model   delta    sigma   weight residual
     110.92  103.31    7.61 1.59e+00 3.96e-01 2.29e+01
  angle pdb=" C   ASN B 487 "
        pdb=" CA  ASN B 487 "
        pdb=" CB  ASN B 487 "
      ideal   model   delta    sigma   weight residual
     110.42  118.49   -8.07 1.99e+00 2.53e-01 1.65e+01
  angle pdb=" CA  CYS B 488 "
        pdb=" C   CYS B 488 "
        pdb=" O   CYS B 488 "
      ideal   model   delta    sigma   weight residual
     120.66  116.08    4.58 1.15e+00 7.56e-01 1.59e+01
  angle pdb=" N   GLY B 381 "
        pdb=" CA  GLY B 381 "
        pdb=" C   GLY B 381 "
      ideal   model   delta    sigma   weight residual
     115.08  108.96    6.12 1.54e+00 4.22e-01 1.58e+01
  ... (remaining 9091 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 3724
       17.78 -    35.56: 266
       35.56 -    53.34: 35
       53.34 -    71.12: 21
       71.12 -    88.90: 8
  Dihedral angle restraints: 4054
    sinusoidal: 1751
      harmonic: 2303
  Sorted by residual:
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   14.36   78.64     1      1.00e+01 1.00e-02 7.71e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.76   58.24     1      1.00e+01 1.00e-02 4.55e+01
  dihedral pdb=" C   TYR A 243 "
           pdb=" N   TYR A 243 "
           pdb=" CA  TYR A 243 "
           pdb=" CB  TYR A 243 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.26  -11.34     0      2.50e+00 1.60e-01 2.06e+01
  ... (remaining 4051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.184: 965
       0.184 -    0.367: 4
       0.367 -    0.551: 0
       0.551 -    0.734: 0
       0.734 -    0.918: 1
  Chirality restraints: 970
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.03   -0.37 2.00e-02 2.50e+03 3.34e+02
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-02 2.50e+03 7.83e+01
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.69e+01
  ... (remaining 967 not shown)

  Planarity restraints: 1166
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.270 2.00e-02 2.50e+03   2.32e-01 6.73e+02
        pdb=" C7  NAG D   1 "    0.064 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.160 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.406 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "   -0.241 2.00e-02 2.50e+03   2.04e-01 5.21e+02
        pdb=" C7  NAG F   2 "    0.057 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "   -0.159 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "    0.349 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "   -0.150 2.00e-02 2.50e+03   1.25e-01 1.96e+02
        pdb=" C7  NAG A 702 "    0.038 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "   -0.109 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "    0.206 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1163 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1519
        2.79 -     3.32: 5929
        3.32 -     3.84: 9918
        3.84 -     4.37: 11416
        4.37 -     4.90: 19745
  Nonbonded interactions: 48527
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 365 "
            pdb=" OD1 ASP A 367 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER A 109 "
            pdb=" OD1 ASP A 111 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   ASN A 121 "
            pdb=" OG1 THR A 125 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.317 2.230
  nonbonded pdb=" NH1 ARG A 245 "
            pdb=" O   GLY A 605 "
     model   vdw
     2.368 3.120
  ... (remaining 48522 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:             16.630
  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:          0.310
  Check model and map are aligned:         0.120
  Set scattering table:                    0.100
  Process input model:                     21.760
  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:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6758
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      :  0.004   0.068   6693  Z= 0.225
  Angle     :  0.628   9.146   9096  Z= 0.352
  Chirality :  0.055   0.918    970
  Planarity :  0.011   0.232   1161
  Dihedral  : 13.011  88.897   2560
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.12 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  0.29 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.27 %
  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: -0.17 (0.31), residues: 777
  helix:  0.83 (0.29), residues: 340
  sheet:  2.14 (0.93), residues: 38
  loop : -1.21 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 566 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.008   0.001   PHE B 377 
 TYR   0.011   0.001   TYR B 501 
 ARG   0.002   0.000   ARG A  95 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 140
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  474 MET cc_start: 0.7906 (mmp) cc_final: 0.7607 (mmt)
REVERT: B  467 ASP cc_start: 0.6675 (t0) cc_final: 0.6316 (t0)
  outliers start: 4
  outliers final: 1
  residues processed: 142
  average time/residue: 0.2629
  time to fit residues: 46.2977
Evaluate side-chains
  72 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  382 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   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 101 GLN
B 487 ASN
B 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.081756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.069213 restraints weight = 33612.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 9.32
r_work: 0.3438 rms_B_bonded: 8.48 restraints_weight: 2.0000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6693  Z= 0.226
  Angle     :  0.652   7.180   9096  Z= 0.324
  Chirality :  0.043   0.239    970
  Planarity :  0.004   0.049   1161
  Dihedral  :  7.685  58.833   1047
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.25 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  8.26 %
    Favored  : 89.71 %
  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:  0.31 (0.31), residues: 777
  helix:  1.30 (0.29), residues: 345
  sheet:  1.82 (0.88), residues: 38
  loop : -0.97 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.043   0.002   PHE A 525 
 TYR   0.016   0.001   TYR A  50 
 ARG   0.010   0.001   ARG A 582 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 LEU cc_start: 0.9352 (mt) cc_final: 0.9058 (mt)
REVERT: A  462 MET cc_start: 0.9467 (tpp) cc_final: 0.9172 (tpp)
REVERT: A  474 MET cc_start: 0.8946 (mmp) cc_final: 0.8397 (mmt)
REVERT: B  358 ILE cc_start: 0.8378 (mm) cc_final: 0.8044 (mm)
  outliers start: 14
  outliers final: 7
  residues processed: 86
  average time/residue: 0.2454
  time to fit residues: 26.7781
Evaluate side-chains
  72 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  465 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0040
   chunk 72 optimal weight:    0.0020
   chunk 60 optimal weight:    0.7980
   chunk 54 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0870
   chunk 46 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0770
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.1136

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

Flipped N/Q/H residues before XYZ refinement:
** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.082262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.069587 restraints weight = 33901.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 9.13
r_work: 0.3466 rms_B_bonded: 8.16 restraints_weight: 2.0000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6693  Z= 0.155
  Angle     :  0.610  11.434   9096  Z= 0.295
  Chirality :  0.042   0.190    970
  Planarity :  0.004   0.031   1161
  Dihedral  :  7.604  57.555   1046
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.09 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.13 %
    Favored  : 89.71 %
  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:  0.33 (0.31), residues: 777
  helix:  1.15 (0.28), residues: 358
  sheet:  1.74 (0.86), residues: 38
  loop : -0.85 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 378 
 PHE   0.025   0.001   PHE A 525 
 TYR   0.021   0.001   TYR B 423 
 ARG   0.006   0.001   ARG A 219 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.9465 (mmm) cc_final: 0.9077 (mmm)
REVERT: A  267 LEU cc_start: 0.9354 (mt) cc_final: 0.8993 (tt)
REVERT: A  332 MET cc_start: 0.9085 (tmm) cc_final: 0.8860 (tmm)
REVERT: A  462 MET cc_start: 0.9478 (tpp) cc_final: 0.9248 (tpp)
REVERT: A  474 MET cc_start: 0.8915 (mmp) cc_final: 0.8403 (mmp)
REVERT: B  355 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7946 (tpp80)
REVERT: B  358 ILE cc_start: 0.8286 (mm) cc_final: 0.8007 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 80
  average time/residue: 0.1942
  time to fit residues: 21.0404
Evaluate side-chains
  69 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.080181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.067995 restraints weight = 34260.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 8.30
r_work: 0.3434 rms_B_bonded: 7.86 restraints_weight: 2.0000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6693  Z= 0.192
  Angle     :  0.590  10.426   9096  Z= 0.286
  Chirality :  0.041   0.182    970
  Planarity :  0.004   0.032   1161
  Dihedral  :  7.648  56.513   1046
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.96 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.28 %
    Favored  : 89.13 %
  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:  0.27 (0.31), residues: 777
  helix:  1.15 (0.28), residues: 370
  sheet:  1.59 (0.86), residues: 38
  loop : -1.00 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 302 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.018   0.001   PHE A 525 
 TYR   0.016   0.001   TYR B 423 
 ARG   0.007   0.001   ARG B 346 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 LEU cc_start: 0.9365 (mt) cc_final: 0.9046 (mt)
REVERT: A  462 MET cc_start: 0.9459 (tpp) cc_final: 0.9255 (tpp)
REVERT: A  474 MET cc_start: 0.8906 (mmp) cc_final: 0.8419 (mmp)
REVERT: B  358 ILE cc_start: 0.8371 (mm) cc_final: 0.8066 (mm)
  outliers start: 11
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1553
  time to fit residues: 15.4424
Evaluate side-chains
  65 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.078968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.066897 restraints weight = 34209.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 8.12
r_work: 0.3420 rms_B_bonded: 7.70 restraints_weight: 2.0000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6693  Z= 0.202
  Angle     :  0.605  11.508   9096  Z= 0.288
  Chirality :  0.041   0.182    970
  Planarity :  0.003   0.032   1161
  Dihedral  :  7.649  59.605   1046
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.22 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.14 %
    Favored  : 87.83 %
  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:  0.21 (0.31), residues: 777
  helix:  1.06 (0.28), residues: 370
  sheet:  1.46 (0.89), residues: 38
  loop : -0.95 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 302 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.015   0.001   PHE A 525 
 TYR   0.015   0.001   TYR B 423 
 ARG   0.004   0.000   ARG B 346 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 LEU cc_start: 0.9382 (mt) cc_final: 0.9057 (mt)
REVERT: A  474 MET cc_start: 0.8901 (mmp) cc_final: 0.8420 (mmp)
REVERT: B  358 ILE cc_start: 0.8401 (mm) cc_final: 0.8083 (mm)
REVERT: B  398 ASP cc_start: 0.7229 (t0) cc_final: 0.6872 (p0)
  outliers start: 14
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1503
  time to fit residues: 15.2440
Evaluate side-chains
  69 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.078570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.066520 restraints weight = 34417.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 8.30
r_work: 0.3407 rms_B_bonded: 7.85 restraints_weight: 2.0000
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6693  Z= 0.190
  Angle     :  0.587  10.600   9096  Z= 0.279
  Chirality :  0.040   0.180    970
  Planarity :  0.003   0.031   1161
  Dihedral  :  7.580  56.922   1046
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.99 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 10.72 %
    Favored  : 86.96 %
  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:  0.21 (0.31), residues: 777
  helix:  1.06 (0.28), residues: 371
  sheet:  1.42 (0.90), residues: 38
  loop : -0.96 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 302 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.013   0.001   PHE A 525 
 TYR   0.014   0.001   TYR B 423 
 ARG   0.003   0.000   ARG B 346 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 LEU cc_start: 0.9401 (mt) cc_final: 0.9068 (mt)
REVERT: A  474 MET cc_start: 0.8906 (mmp) cc_final: 0.8428 (mmp)
REVERT: B  358 ILE cc_start: 0.8413 (mm) cc_final: 0.8104 (mm)
  outliers start: 16
  outliers final: 11
  residues processed: 71
  average time/residue: 0.1508
  time to fit residues: 15.7399
Evaluate side-chains
  64 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0050
   chunk 18 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0570
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.4112

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.079190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.066990 restraints weight = 34117.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 8.54
r_work: 0.3420 rms_B_bonded: 8.02 restraints_weight: 2.0000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6693  Z= 0.150
  Angle     :  0.610  11.650   9096  Z= 0.281
  Chirality :  0.041   0.184    970
  Planarity :  0.003   0.029   1161
  Dihedral  :  7.513  55.521   1046
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.99 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.59 %
    Favored  : 86.52 %
  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:  0.29 (0.31), residues: 777
  helix:  1.18 (0.28), residues: 365
  sheet:  1.36 (0.90), residues: 38
  loop : -0.94 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 302 
 HIS   0.002   0.001   HIS A 378 
 PHE   0.013   0.001   PHE A 525 
 TYR   0.010   0.001   TYR B 423 
 ARG   0.006   0.000   ARG B 408 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  234 MET cc_start: 0.8886 (tpp) cc_final: 0.8682 (tpp)
REVERT: A  267 LEU cc_start: 0.9405 (mt) cc_final: 0.9071 (mt)
REVERT: A  297 MET cc_start: 0.7939 (mmm) cc_final: 0.7688 (tpt)
REVERT: A  474 MET cc_start: 0.8884 (mmp) cc_final: 0.8402 (mmp)
REVERT: B  358 ILE cc_start: 0.8424 (mm) cc_final: 0.8179 (mm)
REVERT: B  398 ASP cc_start: 0.7095 (t0) cc_final: 0.6716 (m-30)
  outliers start: 13
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1479
  time to fit residues: 14.9436
Evaluate side-chains
  69 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    0.1980
   chunk 43 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.078402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.066188 restraints weight = 34715.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 8.73
r_work: 0.3397 rms_B_bonded: 7.94 restraints_weight: 2.0000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6693  Z= 0.159
  Angle     :  0.576  10.839   9096  Z= 0.271
  Chirality :  0.040   0.175    970
  Planarity :  0.003   0.030   1161
  Dihedral  :  7.461  54.512   1046
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.50 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 11.30 %
    Favored  : 86.52 %
  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:  0.34 (0.32), residues: 777
  helix:  1.19 (0.28), residues: 374
  sheet:  1.28 (0.91), residues: 38
  loop : -0.91 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 302 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.011   0.001   PHE A 525 
 TYR   0.011   0.001   TYR B 423 
 ARG   0.005   0.000   ARG B 408 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 LEU cc_start: 0.9442 (mt) cc_final: 0.9119 (mt)
REVERT: A  474 MET cc_start: 0.8899 (mmp) cc_final: 0.8422 (mmp)
REVERT: B  358 ILE cc_start: 0.8436 (mm) cc_final: 0.8122 (mm)
  outliers start: 15
  outliers final: 14
  residues processed: 71
  average time/residue: 0.1560
  time to fit residues: 15.8742
Evaluate side-chains
  70 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0970
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0270
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.5036

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.078377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.066044 restraints weight = 34674.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 9.44
r_work: 0.3392 rms_B_bonded: 8.22 restraints_weight: 2.0000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6693  Z= 0.155
  Angle     :  0.580  11.022   9096  Z= 0.271
  Chirality :  0.040   0.174    970
  Planarity :  0.003   0.029   1161
  Dihedral  :  7.438  54.510   1046
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.25 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.74 %
    Favored  : 86.38 %
  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:  0.37 (0.32), residues: 777
  helix:  1.21 (0.28), residues: 374
  sheet:  1.38 (0.91), residues: 38
  loop : -0.91 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 302 
 HIS   0.002   0.001   HIS A 378 
 PHE   0.010   0.001   PHE A 525 
 TYR   0.011   0.001   TYR B 423 
 ARG   0.003   0.000   ARG B 346 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 LEU cc_start: 0.9451 (mt) cc_final: 0.9123 (mt)
REVERT: A  474 MET cc_start: 0.8910 (mmp) cc_final: 0.8438 (mmp)
REVERT: B  358 ILE cc_start: 0.8468 (mm) cc_final: 0.8144 (mm)
  outliers start: 13
  outliers final: 13
  residues processed: 70
  average time/residue: 0.1848
  time to fit residues: 18.4141
Evaluate side-chains
  69 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  203 TRP
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 39 optimal weight:    0.0270
   chunk 37 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7442

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.077622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.065558 restraints weight = 35018.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 8.59
r_work: 0.3384 rms_B_bonded: 7.90 restraints_weight: 2.0000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6693  Z= 0.179
  Angle     :  0.580  11.099   9096  Z= 0.275
  Chirality :  0.040   0.169    970
  Planarity :  0.003   0.030   1161
  Dihedral  :  7.445  54.423   1046
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.63 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 11.45 %
    Favored  : 86.23 %
  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:  0.42 (0.31), residues: 777
  helix:  1.23 (0.28), residues: 376
  sheet:  0.94 (0.90), residues: 40
  loop : -0.80 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 302 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.010   0.001   PHE A 525 
 TYR   0.011   0.001   TYR B 423 
 ARG   0.003   0.000   ARG B 408 

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 LEU cc_start: 0.9433 (mt) cc_final: 0.9104 (mt)
REVERT: A  474 MET cc_start: 0.8863 (mmp) cc_final: 0.8431 (mmp)
REVERT: B  358 ILE cc_start: 0.8494 (mm) cc_final: 0.8111 (mm)
REVERT: B  398 ASP cc_start: 0.7281 (t0) cc_final: 0.6851 (p0)
  outliers start: 16
  outliers final: 13
  residues processed: 69
  average time/residue: 0.1455
  time to fit residues: 14.6826
Evaluate side-chains
  67 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0870
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
B 394 ASN
** B 493 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 = 0.3911 r_free = 0.3911 target = 0.078161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.066082 restraints weight = 35213.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 8.30
r_work: 0.3404 rms_B_bonded: 7.83 restraints_weight: 2.0000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6693  Z= 0.152
  Angle     :  0.578  11.518   9096  Z= 0.270
  Chirality :  0.040   0.170    970
  Planarity :  0.003   0.029   1161
  Dihedral  :  7.428  54.430   1046
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.60 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.59 %
    Favored  : 86.67 %
  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:  0.45 (0.31), residues: 777
  helix:  1.24 (0.28), residues: 376
  sheet:  0.98 (0.89), residues: 40
  loop : -0.78 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 302 
 HIS   0.002   0.001   HIS A 378 
 PHE   0.010   0.001   PHE A 525 
 TYR   0.010   0.001   TYR B 423 
 ARG   0.003   0.000   ARG B 408 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5281.55 seconds
wall clock time: 96 minutes 34.17 seconds (5794.17 seconds total)