Starting phenix.real_space_refine
on Thu Mar 13 03:19:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zl4_60218/03_2025/8zl4_60218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zl4_60218/03_2025/8zl4_60218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zl4_60218/03_2025/8zl4_60218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zl4_60218/03_2025/8zl4_60218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zl4_60218/03_2025/8zl4_60218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zl4_60218/03_2025/8zl4_60218.cif"
  }
  resolution = 3.65
  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=   0.056
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       2      5.49       5
     S      88      5.16       5
     C    5702      2.51       5
     N    1352      2.21       5
     O    1452      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8596
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4221
          Classifications: {'peptide': 541}
          Link IDs: {'PTRANS': 33, 'TRANS': 507}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4221
          Classifications: {'peptide': 541}
          Link IDs: {'PTRANS': 33, 'TRANS': 507}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 77
          Unusual residues: {'FLC': 1, 'NAG': 1, 'PTY': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 77
          Unusual residues: {'FLC': 1, 'NAG': 1, 'PTY': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.52, per 1000 atoms: 0.64
  Number of scatterers: 8596
  At special positions: 0
  Unit cell: (87.98, 108.73, 117.03, 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      88     16.00
     P       2     15.00
     O    1452      8.00
     N    1352      7.00
     C    5702      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 0 sheets defined
      83.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 40
      removed outlier: 3.518A  pdb=" N   PHE A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE A  37 " --> pdb=" O   CYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 54
      removed outlier: 3.549A  pdb=" N   LEU A  44 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A  46 " --> pdb=" O   LYS A  42 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 54 through 60
      removed outlier: 3.797A  pdb=" N   LEU A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ASN A  60 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 81
      removed outlier: 3.860A  pdb=" N   ARG A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 89
      removed outlier: 3.678A  pdb=" N   THR A  88 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   SER A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 89'
    Processing helix  chain 'A' and resid 90 through 100
      removed outlier: 4.280A  pdb=" N   VAL A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
    Processing helix  chain 'A' and resid 103 through 110
    Processing helix  chain 'A' and resid 113 through 132
      removed outlier: 3.981A  pdb=" N   CYS A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 147
      removed outlier: 3.575A  pdb=" N   ARG A 137 " --> pdb=" O   ASN A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 166
    Processing helix  chain 'A' and resid 169 through 192
      Proline residue:  A 179  - end of helix
    Processing helix  chain 'A' and resid 220 through 238
      removed outlier: 4.054A  pdb=" N   GLY A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 241
      No H-bonds generated for 'chain 'A' and resid 239 through 241'
    Processing helix  chain 'A' and resid 245 through 259
      removed outlier: 4.020A  pdb=" N   LEU A 249 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 296
      Proline residue:  A 277  - end of helix
    Processing helix  chain 'A' and resid 302 through 314
    Processing helix  chain 'A' and resid 314 through 330
      removed outlier: 3.993A  pdb=" N   GLY A 330 " --> pdb=" O   TYR A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 352
    Processing helix  chain 'A' and resid 360 through 365
    Processing helix  chain 'A' and resid 372 through 386
      removed outlier: 4.373A  pdb=" N   THR A 376 " --> pdb=" O   ASN A 372 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 377 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 397
      removed outlier: 4.069A  pdb=" N   CYS A 396 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 397'
    Processing helix  chain 'A' and resid 413 through 421
      removed outlier: 3.659A  pdb=" N   THR A 419 " --> pdb=" O   LYS A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 443
      removed outlier: 3.706A  pdb=" N   LEU A 428 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLY A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 452
    Processing helix  chain 'A' and resid 453 through 458
      removed outlier: 3.659A  pdb=" N   LYS A 456 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL A 457 " --> pdb=" O   GLY A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 476
    Processing helix  chain 'A' and resid 479 through 498
      Proline residue:  A 489  - end of helix
    Processing helix  chain 'A' and resid 501 through 513
      removed outlier: 4.121A  pdb=" N   LEU A 505 " --> pdb=" O   HIS A 501 " (cutoff:3.500A)
      Proline residue:  A 508  - end of helix
    Processing helix  chain 'A' and resid 523 through 531
    Processing helix  chain 'A' and resid 536 through 544
    Processing helix  chain 'A' and resid 544 through 567
      removed outlier: 3.791A  pdb=" N   THR A 548 " --> pdb=" O   GLY A 544 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A 549 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLN A 560 " --> pdb=" O   PHE A 556 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   THR A 561 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   LEU A 564 " --> pdb=" O   GLN A 560 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL A 565 " --> pdb=" O   THR A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 584
    Processing helix  chain 'B' and resid 33 through 40
    Processing helix  chain 'B' and resid 40 through 53
      removed outlier: 3.615A  pdb=" N   LEU B  44 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 54 through 60
      removed outlier: 3.922A  pdb=" N   LEU B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN B  60 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 81
      removed outlier: 3.719A  pdb=" N   ARG B  66 " --> pdb=" O   GLY B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 89
      removed outlier: 3.735A  pdb=" N   THR B  88 " --> pdb=" O   PRO B  84 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   SER B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 84 through 89'
    Processing helix  chain 'B' and resid 91 through 100
      Proline residue:  B  97  - end of helix
    Processing helix  chain 'B' and resid 103 through 111
      removed outlier: 3.996A  pdb=" N   TYR B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 132
      removed outlier: 3.834A  pdb=" N   VAL B 117 " --> pdb=" O   LYS B 113 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   CYS B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 147
      removed outlier: 3.685A  pdb=" N   ARG B 137 " --> pdb=" O   ASN B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 166
    Processing helix  chain 'B' and resid 169 through 192
      Proline residue:  B 179  - end of helix
    Processing helix  chain 'B' and resid 220 through 238
    Processing helix  chain 'B' and resid 239 through 240
      No H-bonds generated for 'chain 'B' and resid 239 through 240'
    Processing helix  chain 'B' and resid 241 through 244
      removed outlier: 3.512A  pdb=" N   GLY B 244 " --> pdb=" O   THR B 241 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 241 through 244'
    Processing helix  chain 'B' and resid 245 through 259
      removed outlier: 3.844A  pdb=" N   LEU B 249 " --> pdb=" O   THR B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 296
      removed outlier: 3.527A  pdb=" N   MET B 272 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      Proline residue:  B 277  - end of helix
      removed outlier: 3.678A  pdb=" N   VAL B 281 " --> pdb=" O   PRO B 277 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLY B 296 " --> pdb=" O   TRP B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 3.855A  pdb=" N   GLN B 306 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU B 307 " --> pdb=" O   LYS B 303 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY B 314 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 330
      removed outlier: 3.999A  pdb=" N   GLY B 330 " --> pdb=" O   TYR B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 353
    Processing helix  chain 'B' and resid 360 through 365
    Processing helix  chain 'B' and resid 372 through 386
      removed outlier: 4.544A  pdb=" N   THR B 376 " --> pdb=" O   ASN B 372 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE B 377 " --> pdb=" O   SER B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 399
      removed outlier: 3.846A  pdb=" N   THR B 397 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 419
      removed outlier: 3.643A  pdb=" N   THR B 419 " --> pdb=" O   LYS B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 443
      removed outlier: 3.594A  pdb=" N   LEU B 428 " --> pdb=" O   GLY B 424 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLY B 443 " --> pdb=" O   SER B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 452
    Processing helix  chain 'B' and resid 453 through 458
      removed outlier: 3.787A  pdb=" N   LYS B 456 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL B 457 " --> pdb=" O   GLY B 454 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B 458 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 453 through 458'
    Processing helix  chain 'B' and resid 459 through 476
    Processing helix  chain 'B' and resid 479 through 499
      Proline residue:  B 489  - end of helix
    Processing helix  chain 'B' and resid 501 through 513
      removed outlier: 4.002A  pdb=" N   LEU B 505 " --> pdb=" O   HIS B 501 " (cutoff:3.500A)
      Proline residue:  B 508  - end of helix
    Processing helix  chain 'B' and resid 523 through 533
      removed outlier: 3.643A  pdb=" N   ALA B 527 " --> pdb=" O   THR B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 544
      removed outlier: 3.685A  pdb=" N   MET B 540 " --> pdb=" O   ARG B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 567
      removed outlier: 3.532A  pdb=" N   THR B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE B 549 " --> pdb=" O   ILE B 545 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLN B 560 " --> pdb=" O   PHE B 556 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   LEU B 564 " --> pdb=" O   GLN B 560 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL B 565 " --> pdb=" O   THR B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 584
      removed outlier: 3.545A  pdb=" N   TYR B 580 " --> pdb=" O   TRP B 576 " (cutoff:3.500A)

    540 hydrogen bonds defined for protein.
    1617 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: 2.54

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1332
        1.32 -     1.45: 2309
        1.45 -     1.57: 5027
        1.57 -     1.69: 4
        1.69 -     1.81: 146
  Bond restraints: 8818
  Sorted by residual:
  bond pdb=" C   LEU B  54 "
       pdb=" N   PRO B  55 "
    ideal  model  delta    sigma   weight residual
    1.336  1.364 -0.029 1.08e-02 8.57e+03 6.99e+00
  bond pdb=" N   VAL B 403 "
       pdb=" CA  VAL B 403 "
    ideal  model  delta    sigma   weight residual
    1.465  1.492 -0.027 1.02e-02 9.61e+03 6.98e+00
  bond pdb=" N   GLY B 401 "
       pdb=" CA  GLY B 401 "
    ideal  model  delta    sigma   weight residual
    1.443  1.479 -0.036 1.37e-02 5.33e+03 6.96e+00
  bond pdb=" N   ARG B 398 "
       pdb=" CA  ARG B 398 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.51e+00
  bond pdb=" N   GLY B 406 "
       pdb=" CA  GLY B 406 "
    ideal  model  delta    sigma   weight residual
    1.443  1.475 -0.032 1.37e-02 5.33e+03 5.61e+00
  ... (remaining 8813 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 11604
        2.13 -     4.25: 322
        4.25 -     6.38: 41
        6.38 -     8.51: 7
        8.51 -    10.63: 4
  Bond angle restraints: 11978
  Sorted by residual:
  angle pdb=" CA  TYR B 282 "
        pdb=" CB  TYR B 282 "
        pdb=" CG  TYR B 282 "
      ideal   model   delta    sigma   weight residual
     113.90  121.02   -7.12 1.80e+00 3.09e-01 1.57e+01
  angle pdb=" CA  GLU A 499 "
        pdb=" CB  GLU A 499 "
        pdb=" CG  GLU A 499 "
      ideal   model   delta    sigma   weight residual
     114.10  121.46   -7.36 2.00e+00 2.50e-01 1.35e+01
  angle pdb=" O11 PTY A 603 "
        pdb=" P1  PTY A 603 "
        pdb=" O14 PTY A 603 "
      ideal   model   delta    sigma   weight residual
      92.90  103.53  -10.63 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" C   PRO B 402 "
        pdb=" CA  PRO B 402 "
        pdb=" CB  PRO B 402 "
      ideal   model   delta    sigma   weight residual
     111.21  106.61    4.60 1.33e+00 5.65e-01 1.20e+01
  angle pdb=" C   VAL B 281 "
        pdb=" N   TYR B 282 "
        pdb=" CA  TYR B 282 "
      ideal   model   delta    sigma   weight residual
     121.14  115.25    5.89 1.75e+00 3.27e-01 1.13e+01
  ... (remaining 11973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.11: 5048
       25.11 -    50.23: 187
       50.23 -    75.34: 16
       75.34 -   100.45: 4
      100.45 -   125.57: 3
  Dihedral angle restraints: 5258
    sinusoidal: 2120
      harmonic: 3138
  Sorted by residual:
  dihedral pdb=" CA  TYR A 111 "
           pdb=" C   TYR A 111 "
           pdb=" N   PHE A 112 "
           pdb=" CA  PHE A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.18  -22.82     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" N1  PTY B 603 "
           pdb=" C2  PTY B 603 "
           pdb=" C3  PTY B 603 "
           pdb=" O11 PTY B 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33  -60.24  125.57     1      3.00e+01 1.11e-03 1.69e+01
  dihedral pdb=" CA  ALA A 516 "
           pdb=" C   ALA A 516 "
           pdb=" N   PHE A 517 "
           pdb=" CA  PHE A 517 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.52  -20.48     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 5255 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1036
       0.050 -    0.101: 277
       0.101 -    0.151: 63
       0.151 -    0.201: 9
       0.201 -    0.252: 3
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CA  TYR B 395 "
            pdb=" N   TYR B 395 "
            pdb=" C   TYR B 395 "
            pdb=" CB  TYR B 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  LEU A 185 "
            pdb=" N   LEU A 185 "
            pdb=" C   LEU A 185 "
            pdb=" CB  LEU A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  TYR A 282 "
            pdb=" N   TYR A 282 "
            pdb=" C   TYR A 282 "
            pdb=" CB  TYR A 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1385 not shown)

  Planarity restraints: 1458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  91 "    0.033 5.00e-02 4.00e+02   5.03e-02 4.04e+00
        pdb=" N   PRO B  92 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B  92 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  92 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 524 "    0.031 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO A 525 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 525 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 525 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  54 "    0.029 5.00e-02 4.00e+02   4.40e-02 3.09e+00
        pdb=" N   PRO A  55 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  55 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  55 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1455 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1951
        2.78 -     3.31: 9145
        3.31 -     3.84: 13722
        3.84 -     4.37: 15232
        4.37 -     4.90: 25583
  Nonbonded interactions: 65633
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 408 "
            pdb=" O12 PTY B 603 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   CYS A 239 "
            pdb=" OG  SER A 275 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NH1 ARG B 151 "
            pdb=" OE1 GLN B 291 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   PRO B 217 "
            pdb=" ND2 ASN B 534 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   ALA A 231 "
            pdb=" OG  SER A 234 "
     model   vdw
     2.316 3.040
  ... (remaining 65628 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.580
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
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      :  0.006   0.064   8818  Z= 0.378
  Angle     :  0.824  10.634  11978  Z= 0.449
  Chirality :  0.049   0.252   1388
  Planarity :  0.005   0.050   1458
  Dihedral  : 13.184 125.565   3238
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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:  0.78 (0.25), residues: 1074
  helix:  1.12 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -1.09 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  78 
 HIS   0.007   0.001   HIS A 335 
 PHE   0.028   0.002   PHE A 378 
 TYR   0.029   0.002   TYR B 282 
 ARG   0.004   0.000   ARG B 137 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A  105 ASP cc_start: 0.9011 (t70) cc_final: 0.8682 (t0)
REVERT: A  114 ASP cc_start: 0.9064 (p0) cc_final: 0.8729 (p0)
REVERT: A  118 MET cc_start: 0.9326 (ttm) cc_final: 0.8855 (ttm)
REVERT: A  186 GLU cc_start: 0.8720 (pp20) cc_final: 0.8399 (pp20)
REVERT: A  256 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8435 (mm-30)
REVERT: A  272 MET cc_start: 0.8316 (mmp) cc_final: 0.8042 (mmp)
REVERT: A  395 TYR cc_start: 0.7166 (t80) cc_final: 0.6841 (t80)
REVERT: A  532 TYR cc_start: 0.7489 (t80) cc_final: 0.7200 (t80)
REVERT: A  562 TRP cc_start: 0.8551 (t-100) cc_final: 0.8073 (t-100)
REVERT: B  127 LEU cc_start: 0.9742 (mm) cc_final: 0.9526 (mm)
REVERT: B  323 ASP cc_start: 0.9106 (p0) cc_final: 0.8838 (p0)
REVERT: B  382 MET cc_start: 0.9401 (tpp) cc_final: 0.9052 (tpp)
REVERT: B  539 ASP cc_start: 0.9311 (m-30) cc_final: 0.9107 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1519
  time to fit residues: 52.4597
Evaluate side-chains
  184 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 248 ASN
A 518 HIS
B  40 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.090216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.066608 restraints weight = 23337.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.068935 restraints weight = 12123.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.070541 restraints weight = 8173.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8818  Z= 0.267
  Angle     :  0.681   7.538  11978  Z= 0.363
  Chirality :  0.044   0.194   1388
  Planarity :  0.005   0.062   1458
  Dihedral  :  9.193 107.206   1288
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 11.00 %
    Favored  : 86.60 %
  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:  1.14 (0.26), residues: 1074
  helix:  1.44 (0.18), residues: 802
  sheet:  None (None), residues: 0
  loop : -1.28 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 292 
 HIS   0.005   0.001   HIS B  40 
 PHE   0.032   0.002   PHE A 378 
 TYR   0.047   0.002   TYR A 282 
 ARG   0.003   0.000   ARG B 137 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8774 (t70) cc_final: 0.8428 (t0)
REVERT: A  114 ASP cc_start: 0.8983 (p0) cc_final: 0.8647 (p0)
REVERT: A  118 MET cc_start: 0.9186 (ttm) cc_final: 0.8975 (ttm)
REVERT: A  166 MET cc_start: 0.8949 (ttm) cc_final: 0.8739 (ttm)
REVERT: A  177 MET cc_start: 0.9212 (tpp) cc_final: 0.8941 (tpp)
REVERT: A  256 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8618 (mm-30)
REVERT: A  295 MET cc_start: 0.8362 (mtt) cc_final: 0.8123 (mtt)
REVERT: A  350 TYR cc_start: 0.8226 (m-80) cc_final: 0.8006 (m-80)
REVERT: A  395 TYR cc_start: 0.7067 (t80) cc_final: 0.6758 (t80)
REVERT: A  532 TYR cc_start: 0.7556 (t80) cc_final: 0.6988 (t80)
REVERT: A  562 TRP cc_start: 0.8644 (t-100) cc_final: 0.8069 (t-100)
REVERT: B   68 MET cc_start: 0.9105 (ttt) cc_final: 0.8726 (ttp)
REVERT: B   81 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: B  201 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7224 (tm-30)
REVERT: B  323 ASP cc_start: 0.9068 (p0) cc_final: 0.8793 (p0)
REVERT: B  382 MET cc_start: 0.9330 (tpp) cc_final: 0.8993 (tpp)
REVERT: B  539 ASP cc_start: 0.9284 (m-30) cc_final: 0.9083 (m-30)
  outliers start: 22
  outliers final: 17
  residues processed: 208
  average time/residue: 0.1519
  time to fit residues: 47.6126
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 183
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 526 ASN
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.093001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.070865 restraints weight = 22610.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.073343 restraints weight = 11229.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.075026 restraints weight = 7281.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8818  Z= 0.208
  Angle     :  0.639   8.332  11978  Z= 0.334
  Chirality :  0.042   0.190   1388
  Planarity :  0.005   0.063   1458
  Dihedral  :  8.230 104.384   1288
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.83 %
    Favored  : 83.33 %
  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:  1.32 (0.26), residues: 1074
  helix:  1.61 (0.18), residues: 802
  sheet:  None (None), residues: 0
  loop : -1.34 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 292 
 HIS   0.008   0.001   HIS B  40 
 PHE   0.024   0.001   PHE A 251 
 TYR   0.040   0.002   TYR A 282 
 ARG   0.001   0.000   ARG A 299 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 206
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8803 (t70) cc_final: 0.8459 (t0)
REVERT: A  114 ASP cc_start: 0.8973 (p0) cc_final: 0.8609 (p0)
REVERT: A  159 MET cc_start: 0.9166 (tpp) cc_final: 0.8845 (mmm)
REVERT: A  186 GLU cc_start: 0.8714 (pp20) cc_final: 0.8371 (pp20)
REVERT: A  256 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: A  374 MET cc_start: 0.8860 (tmm) cc_final: 0.8647 (tmm)
REVERT: A  382 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8345 (mpp)
REVERT: A  395 TYR cc_start: 0.7011 (t80) cc_final: 0.6751 (t80)
REVERT: A  532 TYR cc_start: 0.7627 (t80) cc_final: 0.7354 (t80)
REVERT: A  562 TRP cc_start: 0.8667 (t-100) cc_final: 0.8036 (t-100)
REVERT: B   81 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8469 (tm-30)
REVERT: B  112 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8249 (m-80)
REVERT: B  201 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7223 (tm-30)
REVERT: B  295 MET cc_start: 0.9068 (mmm) cc_final: 0.8576 (mmm)
REVERT: B  323 ASP cc_start: 0.9053 (p0) cc_final: 0.8763 (p0)
REVERT: B  371 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7634 (mpt180)
REVERT: B  382 MET cc_start: 0.9327 (tpp) cc_final: 0.9068 (tpp)
  outliers start: 26
  outliers final: 17
  residues processed: 217
  average time/residue: 0.1489
  time to fit residues: 49.2576
Evaluate side-chains
  205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
** B  40 HIS ** 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 = 0.3360 r_free = 0.3360 target = 0.091216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.067890 restraints weight = 22810.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.070334 restraints weight = 11869.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.071871 restraints weight = 7909.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8818  Z= 0.267
  Angle     :  0.654  10.274  11978  Z= 0.343
  Chirality :  0.043   0.213   1388
  Planarity :  0.005   0.065   1458
  Dihedral  :  7.862  92.808   1288
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.10 %
    Favored  : 79.52 %
  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:  1.29 (0.26), residues: 1074
  helix:  1.58 (0.18), residues: 802
  sheet:  None (None), residues: 0
  loop : -1.33 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 292 
 HIS   0.005   0.001   HIS B  40 
 PHE   0.022   0.001   PHE A 251 
 TYR   0.034   0.002   TYR A 282 
 ARG   0.002   0.000   ARG B 137 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 190
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8815 (t70) cc_final: 0.8429 (t0)
REVERT: A  114 ASP cc_start: 0.8999 (p0) cc_final: 0.8676 (p0)
REVERT: A  159 MET cc_start: 0.9184 (tpp) cc_final: 0.8960 (mmm)
REVERT: A  256 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8663 (mm-30)
REVERT: A  332 MET cc_start: 0.8962 (tpp) cc_final: 0.8622 (mmt)
REVERT: A  374 MET cc_start: 0.8926 (tmm) cc_final: 0.8723 (tmm)
REVERT: A  395 TYR cc_start: 0.7082 (t80) cc_final: 0.6787 (t80)
REVERT: A  532 TYR cc_start: 0.7727 (t80) cc_final: 0.7351 (t80)
REVERT: A  562 TRP cc_start: 0.8683 (t-100) cc_final: 0.8022 (t-100)
REVERT: B   81 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8603 (tm-30)
REVERT: B  112 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8301 (m-80)
REVERT: B  201 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7249 (tm-30)
REVERT: B  323 ASP cc_start: 0.9061 (p0) cc_final: 0.8764 (p0)
REVERT: B  371 ARG cc_start: 0.8096 (tpp-160) cc_final: 0.7644 (mpt180)
REVERT: B  382 MET cc_start: 0.9363 (tpp) cc_final: 0.9074 (tpp)
  outliers start: 31
  outliers final: 24
  residues processed: 204
  average time/residue: 0.1440
  time to fit residues: 44.4501
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0370
   chunk 5 optimal weight:    0.0040
   chunk 26 optimal weight:    8.9990
   chunk 86 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 90 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    0.5670

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B  40 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.094941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.072305 restraints weight = 22124.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.074851 restraints weight = 11141.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.076611 restraints weight = 7305.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8818  Z= 0.163
  Angle     :  0.640  12.536  11978  Z= 0.327
  Chirality :  0.042   0.185   1388
  Planarity :  0.005   0.067   1458
  Dihedral  :  7.488  80.560   1288
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.17 %
    Favored  : 77.89 %
  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:  1.39 (0.26), residues: 1074
  helix:  1.66 (0.18), residues: 804
  sheet:  None (None), residues: 0
  loop : -1.37 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 292 
 HIS   0.006   0.001   HIS B  40 
 PHE   0.018   0.001   PHE A 251 
 TYR   0.033   0.001   TYR A 282 
 ARG   0.002   0.000   ARG A 371 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 211
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8781 (t70) cc_final: 0.8534 (t0)
REVERT: A  114 ASP cc_start: 0.8876 (p0) cc_final: 0.8499 (p0)
REVERT: A  135 HIS cc_start: 0.8479 (p-80) cc_final: 0.8042 (p-80)
REVERT: A  159 MET cc_start: 0.9129 (tpp) cc_final: 0.8925 (mmm)
REVERT: A  256 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8652 (mm-30)
REVERT: A  332 MET cc_start: 0.8968 (tpp) cc_final: 0.8656 (mmt)
REVERT: A  349 MET cc_start: 0.8915 (tpt) cc_final: 0.8352 (tpp)
REVERT: A  382 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8172 (mtm)
REVERT: A  395 TYR cc_start: 0.6966 (t80) cc_final: 0.6729 (t80)
REVERT: A  458 LEU cc_start: 0.8486 (tp) cc_final: 0.8235 (tt)
REVERT: A  532 TYR cc_start: 0.7769 (t80) cc_final: 0.7344 (t80)
REVERT: A  562 TRP cc_start: 0.8667 (t-100) cc_final: 0.7961 (t-100)
REVERT: B   81 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8603 (tm-30)
REVERT: B  112 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8278 (m-80)
REVERT: B  201 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7231 (tm-30)
REVERT: B  295 MET cc_start: 0.9076 (mmm) cc_final: 0.8784 (mmm)
REVERT: B  323 ASP cc_start: 0.9033 (p0) cc_final: 0.8725 (p0)
REVERT: B  371 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.7786 (mpt180)
REVERT: B  382 MET cc_start: 0.9348 (tpp) cc_final: 0.9068 (tpp)
  outliers start: 27
  outliers final: 20
  residues processed: 220
  average time/residue: 0.1494
  time to fit residues: 49.8806
Evaluate side-chains
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  239 CYS
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.093137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.070398 restraints weight = 22255.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.072857 restraints weight = 11483.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.074497 restraints weight = 7571.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8818  Z= 0.252
  Angle     :  0.673  13.649  11978  Z= 0.345
  Chirality :  0.043   0.193   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.480  75.471   1288
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.26 %
    Favored  : 76.03 %
  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:  1.34 (0.26), residues: 1074
  helix:  1.62 (0.18), residues: 800
  sheet:  None (None), residues: 0
  loop : -1.30 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 292 
 HIS   0.006   0.001   HIS B  40 
 PHE   0.039   0.002   PHE A 378 
 TYR   0.032   0.001   TYR A 282 
 ARG   0.003   0.000   ARG A 151 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8799 (t70) cc_final: 0.8367 (t0)
REVERT: A  114 ASP cc_start: 0.8943 (p0) cc_final: 0.8653 (p0)
REVERT: A  159 MET cc_start: 0.9168 (tpp) cc_final: 0.8958 (mmm)
REVERT: A  256 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8656 (mm-30)
REVERT: A  295 MET cc_start: 0.8130 (mpp) cc_final: 0.7921 (pmm)
REVERT: A  332 MET cc_start: 0.8976 (tpp) cc_final: 0.8601 (mmt)
REVERT: A  372 ASN cc_start: 0.8805 (m-40) cc_final: 0.8543 (m-40)
REVERT: A  382 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8199 (mpp)
REVERT: A  395 TYR cc_start: 0.7005 (t80) cc_final: 0.6742 (t80)
REVERT: A  532 TYR cc_start: 0.7753 (t80) cc_final: 0.7299 (t80)
REVERT: A  562 TRP cc_start: 0.8680 (t-100) cc_final: 0.7970 (t-100)
REVERT: B   81 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8690 (tm-30)
REVERT: B  112 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8345 (m-80)
REVERT: B  114 ASP cc_start: 0.9324 (p0) cc_final: 0.8713 (p0)
REVERT: B  201 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7244 (tm-30)
REVERT: B  323 ASP cc_start: 0.9046 (p0) cc_final: 0.8739 (p0)
REVERT: B  371 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7498 (mpt180)
REVERT: B  382 MET cc_start: 0.9400 (tpp) cc_final: 0.9054 (tpp)
  outliers start: 34
  outliers final: 25
  residues processed: 204
  average time/residue: 0.1486
  time to fit residues: 46.5507
Evaluate side-chains
  214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 187
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  239 CYS
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 3 optimal weight:    0.8980
   chunk 71 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 144 GLN
A 338 GLN
** B  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.093067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.070067 restraints weight = 22507.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.072546 restraints weight = 11571.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.074185 restraints weight = 7633.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8818  Z= 0.229
  Angle     :  0.682  14.016  11978  Z= 0.347
  Chirality :  0.043   0.306   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.477  76.984   1288
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.57 %
    Favored  : 75.16 %
  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:  1.32 (0.26), residues: 1074
  helix:  1.61 (0.18), residues: 798
  sheet:  None (None), residues: 0
  loop : -1.31 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 292 
 HIS   0.003   0.001   HIS B 335 
 PHE   0.036   0.001   PHE A 378 
 TYR   0.030   0.001   TYR A 282 
 ARG   0.001   0.000   ARG B 137 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 196
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8801 (t70) cc_final: 0.8375 (t0)
REVERT: A  114 ASP cc_start: 0.8959 (p0) cc_final: 0.8668 (p0)
REVERT: A  159 MET cc_start: 0.9161 (tpp) cc_final: 0.8949 (mmm)
REVERT: A  256 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8651 (mm-30)
REVERT: A  332 MET cc_start: 0.8971 (tpp) cc_final: 0.8559 (mmt)
REVERT: A  382 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8398 (mtm)
REVERT: A  395 TYR cc_start: 0.7003 (t80) cc_final: 0.6736 (t80)
REVERT: A  532 TYR cc_start: 0.7753 (t80) cc_final: 0.7278 (t80)
REVERT: A  562 TRP cc_start: 0.8681 (t-100) cc_final: 0.7945 (t-100)
REVERT: B   37 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.9012 (m-80)
REVERT: B   81 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8721 (tm-30)
REVERT: B  112 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8365 (m-80)
REVERT: B  114 ASP cc_start: 0.9317 (p0) cc_final: 0.8809 (p0)
REVERT: B  295 MET cc_start: 0.9027 (mmm) cc_final: 0.8686 (mmm)
REVERT: B  323 ASP cc_start: 0.9036 (p0) cc_final: 0.8724 (p0)
REVERT: B  346 MET cc_start: 0.9488 (tmm) cc_final: 0.9284 (tmm)
REVERT: B  371 ARG cc_start: 0.8082 (tpp-160) cc_final: 0.7507 (mpt180)
REVERT: B  382 MET cc_start: 0.9416 (tpp) cc_final: 0.9032 (tpp)
  outliers start: 30
  outliers final: 25
  residues processed: 210
  average time/residue: 0.1484
  time to fit residues: 47.3039
Evaluate side-chains
  212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  239 CYS
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0170
   chunk 105 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.2024

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 GLN
** B  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.094033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.071050 restraints weight = 22595.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.073519 restraints weight = 11494.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.075270 restraints weight = 7566.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8818  Z= 0.183
  Angle     :  0.678  14.727  11978  Z= 0.343
  Chirality :  0.042   0.208   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.387  76.748   1288
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.46 %
    Favored  : 74.95 %
  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:  1.34 (0.26), residues: 1074
  helix:  1.63 (0.18), residues: 798
  sheet:  None (None), residues: 0
  loop : -1.31 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 562 
 HIS   0.003   0.001   HIS B 335 
 PHE   0.032   0.001   PHE A 378 
 TYR   0.030   0.001   TYR B 282 
 ARG   0.001   0.000   ARG A 353 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 202
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8801 (t70) cc_final: 0.8378 (t0)
REVERT: A  114 ASP cc_start: 0.8917 (p0) cc_final: 0.8619 (p0)
REVERT: A  159 MET cc_start: 0.9142 (tpp) cc_final: 0.8939 (mmm)
REVERT: A  256 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8622 (mm-30)
REVERT: A  332 MET cc_start: 0.8928 (tpp) cc_final: 0.8647 (mmt)
REVERT: A  382 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8367 (mtm)
REVERT: A  395 TYR cc_start: 0.6973 (t80) cc_final: 0.6700 (t80)
REVERT: A  532 TYR cc_start: 0.7825 (t80) cc_final: 0.7340 (t80)
REVERT: A  562 TRP cc_start: 0.8685 (t-100) cc_final: 0.7907 (t-100)
REVERT: B   37 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.9035 (m-80)
REVERT: B  112 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8317 (m-80)
REVERT: B  114 ASP cc_start: 0.9292 (p0) cc_final: 0.8843 (p0)
REVERT: B  201 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7011 (tm-30)
REVERT: B  295 MET cc_start: 0.9020 (mmm) cc_final: 0.8669 (mmm)
REVERT: B  323 ASP cc_start: 0.9035 (p0) cc_final: 0.8716 (p0)
REVERT: B  345 PHE cc_start: 0.9415 (t80) cc_final: 0.9123 (t80)
REVERT: B  346 MET cc_start: 0.9492 (tmm) cc_final: 0.9275 (tmm)
REVERT: B  371 ARG cc_start: 0.8026 (tpp-160) cc_final: 0.7482 (mpt180)
REVERT: B  382 MET cc_start: 0.9413 (tpp) cc_final: 0.9019 (tpp)
  outliers start: 33
  outliers final: 25
  residues processed: 216
  average time/residue: 0.1423
  time to fit residues: 47.0523
Evaluate side-chains
  227 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  239 CYS
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0970
   chunk 69 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 95 optimal weight:    0.0170
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
** B  39 ASN ** 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 = 0.3436 r_free = 0.3436 target = 0.096040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.072690 restraints weight = 22546.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.075287 restraints weight = 11493.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.076985 restraints weight = 7535.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8818  Z= 0.170
  Angle     :  0.723  15.240  11978  Z= 0.355
  Chirality :  0.043   0.188   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.242  75.067   1288
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.00 %
    Favored  : 75.05 %
  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:  1.29 (0.26), residues: 1074
  helix:  1.59 (0.18), residues: 798
  sheet:  None (None), residues: 0
  loop : -1.31 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 562 
 HIS   0.003   0.001   HIS B 335 
 PHE   0.033   0.001   PHE A 378 
 TYR   0.032   0.001   TYR B 282 
 ARG   0.001   0.000   ARG B 137 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 215
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 MET cc_start: 0.8991 (mmp) cc_final: 0.8754 (mmp)
REVERT: A  105 ASP cc_start: 0.8777 (t70) cc_final: 0.8472 (t0)
REVERT: A  114 ASP cc_start: 0.8902 (p0) cc_final: 0.8590 (p0)
REVERT: A  256 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8613 (mm-30)
REVERT: A  266 MET cc_start: 0.7862 (ttm) cc_final: 0.7428 (ttm)
REVERT: A  349 MET cc_start: 0.8941 (tpt) cc_final: 0.8451 (tpp)
REVERT: A  382 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8385 (mtm)
REVERT: A  395 TYR cc_start: 0.6959 (t80) cc_final: 0.6704 (t80)
REVERT: A  444 MET cc_start: 0.9278 (ppp) cc_final: 0.9067 (ppp)
REVERT: A  532 TYR cc_start: 0.7906 (t80) cc_final: 0.7417 (t80)
REVERT: A  562 TRP cc_start: 0.8675 (t-100) cc_final: 0.7874 (t-100)
REVERT: B   37 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.9001 (m-80)
REVERT: B  112 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8241 (m-80)
REVERT: B  114 ASP cc_start: 0.9276 (p0) cc_final: 0.8956 (p0)
REVERT: B  127 LEU cc_start: 0.9739 (mm) cc_final: 0.9511 (mm)
REVERT: B  201 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7292 (pp30)
REVERT: B  295 MET cc_start: 0.8997 (mmm) cc_final: 0.8691 (mmm)
REVERT: B  323 ASP cc_start: 0.9039 (p0) cc_final: 0.8725 (p0)
REVERT: B  345 PHE cc_start: 0.9383 (t80) cc_final: 0.9098 (t80)
REVERT: B  346 MET cc_start: 0.9511 (tmm) cc_final: 0.9280 (tmm)
REVERT: B  371 ARG cc_start: 0.8014 (tpp-160) cc_final: 0.7448 (mpt180)
REVERT: B  382 MET cc_start: 0.9385 (tpp) cc_final: 0.9013 (tpp)
  outliers start: 27
  outliers final: 20
  residues processed: 228
  average time/residue: 0.1550
  time to fit residues: 53.5565
Evaluate side-chains
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  239 CYS
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0980
   chunk 39 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 GLN
A 485 ASN
** B  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.096152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.073304 restraints weight = 22106.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.075791 restraints weight = 11200.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.077543 restraints weight = 7355.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8818  Z= 0.185
  Angle     :  0.735  15.384  11978  Z= 0.359
  Chirality :  0.043   0.187   1388
  Planarity :  0.005   0.065   1458
  Dihedral  :  7.170  73.616   1288
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.86 %
    Favored  : 73.64 %
  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:  1.30 (0.26), residues: 1074
  helix:  1.54 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop : -1.24 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 562 
 HIS   0.009   0.001   HIS A 335 
 PHE   0.029   0.001   PHE A 378 
 TYR   0.031   0.001   TYR B 282 
 ARG   0.002   0.000   ARG A 141 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 207
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8773 (t70) cc_final: 0.8477 (t0)
REVERT: A  114 ASP cc_start: 0.8943 (p0) cc_final: 0.8640 (p0)
REVERT: A  256 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8591 (mm-30)
REVERT: A  266 MET cc_start: 0.7866 (ttm) cc_final: 0.7553 (ttm)
REVERT: A  349 MET cc_start: 0.8942 (tpt) cc_final: 0.8448 (tpp)
REVERT: A  382 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8465 (mtm)
REVERT: A  395 TYR cc_start: 0.6977 (t80) cc_final: 0.6712 (t80)
REVERT: A  444 MET cc_start: 0.9269 (ppp) cc_final: 0.9051 (ppp)
REVERT: A  532 TYR cc_start: 0.7883 (t80) cc_final: 0.7462 (t80)
REVERT: B   37 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.9029 (m-80)
REVERT: B  112 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8260 (m-80)
REVERT: B  114 ASP cc_start: 0.9268 (p0) cc_final: 0.8930 (p0)
REVERT: B  201 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7061 (tm-30)
REVERT: B  323 ASP cc_start: 0.9045 (p0) cc_final: 0.8737 (p0)
REVERT: B  371 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.7528 (mpt180)
REVERT: B  382 MET cc_start: 0.9342 (tpp) cc_final: 0.9044 (tpp)
  outliers start: 23
  outliers final: 19
  residues processed: 220
  average time/residue: 0.1456
  time to fit residues: 48.7428
Evaluate side-chains
  222 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  239 CYS
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  201 GLN
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  569 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0030
   chunk 66 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7996

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.095741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.072349 restraints weight = 22457.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.074822 restraints weight = 11289.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.076587 restraints weight = 7467.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.177   8818  Z= 0.334
  Angle     :  1.113  59.140  11978  Z= 0.642
  Chirality :  0.045   0.441   1388
  Planarity :  0.007   0.159   1458
  Dihedral  :  7.176  73.607   1288
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 23.97 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.10 %
  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:  1.28 (0.26), residues: 1074
  helix:  1.53 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop : -1.27 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 562 
 HIS   0.010   0.001   HIS A 335 
 PHE   0.025   0.001   PHE A 378 
 TYR   0.030   0.001   TYR B 282 
 ARG   0.002   0.000   ARG A 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2671.44 seconds
wall clock time: 47 minutes 14.46 seconds (2834.46 seconds total)