Starting phenix.real_space_refine
on Thu Feb 13 01:37:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zl4_60218/02_2025/8zl4_60218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zl4_60218/02_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_60218/02_2025/8zl4_60218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zl4_60218/02_2025/8zl4_60218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zl4_60218/02_2025/8zl4_60218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zl4_60218/02_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-5592/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: 5.40, per 1000 atoms: 0.63
  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: 2.48
  Conformation dependent library (CDL) restraints added in 963.9 milliseconds
  

  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: 0.92
  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: 2.32

  Time building geometry restraints manager: 2.78 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: 0.04
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:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.290
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.190
-------------------------------------------------------------------------------
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  : 0.941 
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: 0.1497
  time to fit residues: 51.5505
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  : 0.918 
-------------------------------------------------------------------------------
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 = 0.3351 r_free = 0.3351 target = 0.090066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.066940 restraints weight = 23244.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.069295 restraints weight = 11872.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.070878 restraints weight = 7895.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
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  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8769 (t70) cc_final: 0.8426 (t0)
REVERT: A  114 ASP cc_start: 0.8992 (p0) cc_final: 0.8655 (p0)
REVERT: A  118 MET cc_start: 0.9198 (ttm) cc_final: 0.8989 (ttm)
REVERT: A  166 MET cc_start: 0.8938 (ttm) cc_final: 0.8729 (ttm)
REVERT: A  177 MET cc_start: 0.9222 (tpp) cc_final: 0.8950 (tpp)
REVERT: A  256 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8622 (mm-30)
REVERT: A  295 MET cc_start: 0.8381 (mtt) cc_final: 0.8131 (mtt)
REVERT: A  350 TYR cc_start: 0.8216 (m-80) cc_final: 0.7997 (m-80)
REVERT: A  395 TYR cc_start: 0.7077 (t80) cc_final: 0.6764 (t80)
REVERT: A  532 TYR cc_start: 0.7556 (t80) cc_final: 0.6982 (t80)
REVERT: A  562 TRP cc_start: 0.8650 (t-100) cc_final: 0.8070 (t-100)
REVERT: B   68 MET cc_start: 0.9112 (ttt) cc_final: 0.8734 (ttp)
REVERT: B   81 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8300 (tm-30)
REVERT: B  201 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: B  323 ASP cc_start: 0.9077 (p0) cc_final: 0.8800 (p0)
REVERT: B  382 MET cc_start: 0.9347 (tpp) cc_final: 0.8998 (tpp)
REVERT: B  539 ASP cc_start: 0.9286 (m-30) cc_final: 0.9085 (m-30)
  outliers start: 22
  outliers final: 17
  residues processed: 208
  average time/residue: 0.1642
  time to fit residues: 51.6373
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  : 1.085 
-------------------------------------------------------------------------------
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:    4.9990
   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:    8.9990
   chunk 33 optimal weight:    0.1980
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3391 r_free = 0.3391 target = 0.093124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.070474 restraints weight = 22671.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.072953 restraints weight = 11382.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.074725 restraints weight = 7449.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1587

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= 0.201
  Angle     :  0.636   8.315  11978  Z= 0.332
  Chirality :  0.042   0.189   1388
  Planarity :  0.005   0.063   1458
  Dihedral  :  8.227 104.586   1288
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.62 %
    Favored  : 83.55 %
  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:  1.33 (0.26), residues: 1074
  helix:  1.62 (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   0.011   0.001   TRP B 292 
 HIS   0.014   0.001   HIS B  40 
 PHE   0.024   0.001   PHE A 251 
 TYR   0.039   0.002   TYR A 282 
 ARG   0.001   0.000   ARG B 137 

*********************** 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
  231 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 205
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8801 (t70) cc_final: 0.8457 (t0)
REVERT: A  114 ASP cc_start: 0.8978 (p0) cc_final: 0.8621 (p0)
REVERT: A  159 MET cc_start: 0.9165 (tpp) cc_final: 0.8845 (mmm)
REVERT: A  186 GLU cc_start: 0.8732 (pp20) cc_final: 0.8384 (pp20)
REVERT: A  256 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8614 (mm-30)
REVERT: A  374 MET cc_start: 0.8855 (tmm) cc_final: 0.8645 (tmm)
REVERT: A  382 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8334 (mpp)
REVERT: A  395 TYR cc_start: 0.7013 (t80) cc_final: 0.6754 (t80)
REVERT: A  532 TYR cc_start: 0.7634 (t80) cc_final: 0.7356 (t80)
REVERT: A  562 TRP cc_start: 0.8666 (t-100) cc_final: 0.8030 (t-100)
REVERT: B   81 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8466 (tm-30)
REVERT: B  112 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8315 (m-80)
REVERT: B  201 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7226 (tm-30)
REVERT: B  295 MET cc_start: 0.9089 (mmm) cc_final: 0.8604 (mmm)
REVERT: B  323 ASP cc_start: 0.9053 (p0) cc_final: 0.8763 (p0)
REVERT: B  371 ARG cc_start: 0.8091 (tpp-160) cc_final: 0.7634 (mpt180)
REVERT: B  382 MET cc_start: 0.9320 (tpp) cc_final: 0.9066 (tpp)
  outliers start: 26
  outliers final: 16
  residues processed: 216
  average time/residue: 0.1550
  time to fit residues: 50.8916
Evaluate side-chains
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
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 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:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.091252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.068385 restraints weight = 22647.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.070838 restraints weight = 11713.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.072378 restraints weight = 7746.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8818  Z= 0.239
  Angle     :  0.647  10.246  11978  Z= 0.337
  Chirality :  0.043   0.219   1388
  Planarity :  0.005   0.065   1458
  Dihedral  :  7.776  91.003   1288
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.78 %
    Favored  : 79.74 %
  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:  1.33 (0.26), residues: 1074
  helix:  1.62 (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   0.006   0.001   HIS B  40 
 PHE   0.022   0.001   PHE A 251 
 TYR   0.035   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
  229 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 197
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8799 (t70) cc_final: 0.8418 (t0)
REVERT: A  114 ASP cc_start: 0.8984 (p0) cc_final: 0.8648 (p0)
REVERT: A  159 MET cc_start: 0.9182 (tpp) cc_final: 0.8961 (mmm)
REVERT: A  256 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8682 (mm-30)
REVERT: A  332 MET cc_start: 0.8965 (tpp) cc_final: 0.8629 (mmt)
REVERT: A  374 MET cc_start: 0.8912 (tmm) cc_final: 0.8690 (tmm)
REVERT: A  395 TYR cc_start: 0.7050 (t80) cc_final: 0.6766 (t80)
REVERT: A  532 TYR cc_start: 0.7716 (t80) cc_final: 0.7343 (t80)
REVERT: A  562 TRP cc_start: 0.8677 (t-100) cc_final: 0.8009 (t-100)
REVERT: B  112 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8296 (m-80)
REVERT: B  201 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7204 (tm-30)
REVERT: B  323 ASP cc_start: 0.9057 (p0) cc_final: 0.8759 (p0)
REVERT: B  371 ARG cc_start: 0.8077 (tpp-160) cc_final: 0.7632 (mpt180)
REVERT: B  382 MET cc_start: 0.9358 (tpp) cc_final: 0.9073 (tpp)
  outliers start: 32
  outliers final: 24
  residues processed: 211
  average time/residue: 0.1532
  time to fit residues: 48.6688
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  : 0.946 
-------------------------------------------------------------------------------
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  249 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  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0970
   chunk 100 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    0.3980
   chunk 26 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 90 optimal weight:    0.0870
   chunk 10 optimal weight:    8.9990
   overall best weight:    0.4756

-------------------------------------------------------------------------------
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 = 0.3422 r_free = 0.3422 target = 0.094904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.072012 restraints weight = 22162.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.074553 restraints weight = 11229.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.076313 restraints weight = 7376.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2123

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= 0.162
  Angle     :  0.652  12.665  11978  Z= 0.335
  Chirality :  0.042   0.182   1388
  Planarity :  0.005   0.067   1458
  Dihedral  :  7.473  80.373   1288
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.83 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.26), residues: 1074
  helix:  1.65 (0.18), residues: 802
  sheet:  None (None), residues: 0
  loop : -1.43 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 292 
 HIS   0.003   0.001   HIS A 335 
 PHE   0.018   0.001   PHE A 251 
 TYR   0.053   0.001   TYR A 282 
 ARG   0.001   0.000   ARG A 353 

*********************** 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
  236 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8785 (t70) cc_final: 0.8444 (t0)
REVERT: A  114 ASP cc_start: 0.8861 (p0) cc_final: 0.8470 (p0)
REVERT: A  135 HIS cc_start: 0.8475 (p-80) cc_final: 0.8035 (p-80)
REVERT: A  159 MET cc_start: 0.9131 (tpp) cc_final: 0.8919 (mmm)
REVERT: A  256 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8653 (mm-30)
REVERT: A  332 MET cc_start: 0.8968 (tpp) cc_final: 0.8664 (mmt)
REVERT: A  349 MET cc_start: 0.8918 (tpt) cc_final: 0.8356 (tpp)
REVERT: A  382 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8226 (mtm)
REVERT: A  395 TYR cc_start: 0.6970 (t80) cc_final: 0.6741 (t80)
REVERT: A  501 HIS cc_start: 0.8847 (t70) cc_final: 0.8469 (t-170)
REVERT: A  532 TYR cc_start: 0.7781 (t80) cc_final: 0.7371 (t80)
REVERT: A  562 TRP cc_start: 0.8665 (t-100) cc_final: 0.7955 (t-100)
REVERT: B  112 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8273 (m-80)
REVERT: B  201 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7209 (tm-30)
REVERT: B  295 MET cc_start: 0.9075 (mmm) cc_final: 0.8785 (mmm)
REVERT: B  323 ASP cc_start: 0.9034 (p0) cc_final: 0.8725 (p0)
REVERT: B  371 ARG cc_start: 0.8021 (tpp-160) cc_final: 0.7590 (mpt180)
REVERT: B  382 MET cc_start: 0.9343 (tpp) cc_final: 0.9049 (tpp)
  outliers start: 23
  outliers final: 19
  residues processed: 222
  average time/residue: 0.1488
  time to fit residues: 50.2757
Evaluate side-chains
  214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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  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 A residue  558 PHE
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  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:    0.3980
   chunk 92 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 41 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.092311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.069533 restraints weight = 22486.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.071973 restraints weight = 11680.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.073650 restraints weight = 7753.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2180

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= 0.247
  Angle     :  0.676  13.262  11978  Z= 0.346
  Chirality :  0.043   0.208   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.451  75.583   1288
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.48 %
    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:  1.37 (0.26), residues: 1074
  helix:  1.65 (0.18), residues: 798
  sheet:  None (None), residues: 0
  loop : -1.32 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 292 
 HIS   0.007   0.001   HIS B  40 
 PHE   0.039   0.001   PHE A 378 
 TYR   0.053   0.002   TYR A 282 
 ARG   0.002   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
  227 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 195
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8788 (t70) cc_final: 0.8375 (t0)
REVERT: A  114 ASP cc_start: 0.8900 (p0) cc_final: 0.8606 (p0)
REVERT: A  159 MET cc_start: 0.9151 (tpp) cc_final: 0.8945 (mmm)
REVERT: A  256 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8652 (mm-30)
REVERT: A  332 MET cc_start: 0.8968 (tpp) cc_final: 0.8610 (mmt)
REVERT: A  382 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8219 (mpp)
REVERT: A  395 TYR cc_start: 0.6997 (t80) cc_final: 0.6738 (t80)
REVERT: A  532 TYR cc_start: 0.7761 (t80) cc_final: 0.7330 (t80)
REVERT: A  562 TRP cc_start: 0.8684 (t-100) cc_final: 0.7972 (t-100)
REVERT: B  112 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8318 (m-80)
REVERT: B  201 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7236 (tm-30)
REVERT: B  323 ASP cc_start: 0.9048 (p0) cc_final: 0.8740 (p0)
REVERT: B  371 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7561 (mpt180)
REVERT: B  382 MET cc_start: 0.9394 (tpp) cc_final: 0.9043 (tpp)
  outliers start: 32
  outliers final: 26
  residues processed: 206
  average time/residue: 0.1537
  time to fit residues: 47.7703
Evaluate side-chains
  214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 186
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
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  116 LEU
Chi-restraints excluded: chain A residue  129 VAL
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  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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0060
   chunk 27 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    1.6004

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

Flipped N/Q/H residues before XYZ refinement:
A 144 GLN
B  39 ASN
B  40 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.093653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.071112 restraints weight = 22630.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.073620 restraints weight = 11552.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.075339 restraints weight = 7562.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8818  Z= 0.196
  Angle     :  0.680  13.829  11978  Z= 0.345
  Chirality :  0.043   0.214   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.389  76.938   1288
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.70 %
    Favored  : 75.49 %
  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:  1.36 (0.26), residues: 1074
  helix:  1.65 (0.18), residues: 798
  sheet:  None (None), residues: 0
  loop : -1.30 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 562 
 HIS   0.005   0.001   HIS B  40 
 PHE   0.038   0.001   PHE A 378 
 TYR   0.044   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
  239 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 204
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8794 (t70) cc_final: 0.8541 (t0)
REVERT: A  114 ASP cc_start: 0.8921 (p0) cc_final: 0.8614 (p0)
REVERT: A  159 MET cc_start: 0.9146 (tpp) cc_final: 0.8942 (mmm)
REVERT: A  256 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8625 (mm-30)
REVERT: A  332 MET cc_start: 0.8970 (tpp) cc_final: 0.8566 (mmt)
REVERT: A  395 TYR cc_start: 0.6980 (t80) cc_final: 0.6701 (t80)
REVERT: A  501 HIS cc_start: 0.8869 (t70) cc_final: 0.8494 (t-170)
REVERT: A  532 TYR cc_start: 0.7817 (t80) cc_final: 0.7357 (t80)
REVERT: A  562 TRP cc_start: 0.8684 (t-100) cc_final: 0.7931 (t-100)
REVERT: B   37 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.9016 (m-80)
REVERT: B  112 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8245 (m-80)
REVERT: B  295 MET cc_start: 0.9022 (mmm) cc_final: 0.8740 (mmm)
REVERT: B  323 ASP cc_start: 0.9031 (p0) cc_final: 0.8720 (p0)
REVERT: B  371 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7582 (mpt180)
REVERT: B  382 MET cc_start: 0.9409 (tpp) cc_final: 0.9025 (tpp)
  outliers start: 35
  outliers final: 28
  residues processed: 222
  average time/residue: 0.1551
  time to fit residues: 52.1504
Evaluate side-chains
  225 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 195
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
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  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  338 GLN
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   39 ASN
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  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  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  403 VAL
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:    8.9990
   chunk 106 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 59 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
B 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.094679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.071941 restraints weight = 22627.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.074444 restraints weight = 11410.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.076141 restraints weight = 7452.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8818  Z= 0.198
  Angle     :  0.702  15.023  11978  Z= 0.352
  Chirality :  0.043   0.202   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.343  76.786   1288
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.35 %
    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:  1.32 (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   0.009   0.001   TRP B 562 
 HIS   0.014   0.001   HIS B  40 
 PHE   0.041   0.001   PHE A 378 
 TYR   0.040   0.001   TYR A 282 
 ARG   0.001   0.000   ARG B 137 

*********************** 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: 34
    poor density    : 201
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8804 (t70) cc_final: 0.8486 (t0)
REVERT: A  114 ASP cc_start: 0.8922 (p0) cc_final: 0.8618 (p0)
REVERT: A  256 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: A  332 MET cc_start: 0.8938 (tpp) cc_final: 0.8665 (mmt)
REVERT: A  382 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8439 (mpp)
REVERT: A  395 TYR cc_start: 0.6969 (t80) cc_final: 0.6691 (t80)
REVERT: A  532 TYR cc_start: 0.7816 (t80) cc_final: 0.7338 (t80)
REVERT: A  562 TRP cc_start: 0.8693 (t-100) cc_final: 0.7920 (t-100)
REVERT: B   37 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.9060 (m-80)
REVERT: B  112 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8248 (m-80)
REVERT: B  114 ASP cc_start: 0.9289 (p0) cc_final: 0.8814 (p0)
REVERT: B  201 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7018 (tm-30)
REVERT: B  295 MET cc_start: 0.9017 (mmm) cc_final: 0.8696 (mmm)
REVERT: B  323 ASP cc_start: 0.9039 (p0) cc_final: 0.8719 (p0)
REVERT: B  345 PHE cc_start: 0.9508 (t80) cc_final: 0.9190 (t80)
REVERT: B  371 ARG cc_start: 0.8005 (tpp-160) cc_final: 0.7506 (mpt180)
REVERT: B  382 MET cc_start: 0.9419 (tpp) cc_final: 0.9002 (tpp)
  outliers start: 34
  outliers final: 29
  residues processed: 215
  average time/residue: 0.1485
  time to fit residues: 48.3701
Evaluate side-chains
  229 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 196
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   57 MET
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  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  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   40 HIS
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  403 VAL
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:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 96 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 104 optimal weight:    0.5980
   chunk 95 optimal weight:    0.0570
   overall best weight:    1.1304

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

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
B 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.095161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.072519 restraints weight = 22679.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.075088 restraints weight = 11480.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.076768 restraints weight = 7464.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8818  Z= 0.183
  Angle     :  0.713  15.166  11978  Z= 0.352
  Chirality :  0.043   0.204   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.276  76.294   1288
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.00 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1074
  helix:  1.62 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop : -1.20 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 562 
 HIS   0.018   0.001   HIS B  40 
 PHE   0.035   0.001   PHE A 378 
 TYR   0.043   0.001   TYR A 282 
 ARG   0.001   0.000   ARG B 353 

*********************** 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
  237 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 206
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8795 (t70) cc_final: 0.8481 (t0)
REVERT: A  114 ASP cc_start: 0.8954 (p0) cc_final: 0.8650 (p0)
REVERT: A  256 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8633 (mm-30)
REVERT: A  332 MET cc_start: 0.8907 (tpp) cc_final: 0.8639 (mmt)
REVERT: A  349 MET cc_start: 0.8992 (tpt) cc_final: 0.8560 (tpp)
REVERT: A  395 TYR cc_start: 0.6977 (t80) cc_final: 0.6703 (t80)
REVERT: A  501 HIS cc_start: 0.8810 (t70) cc_final: 0.8527 (t-170)
REVERT: A  532 TYR cc_start: 0.7871 (t80) cc_final: 0.7405 (t80)
REVERT: A  562 TRP cc_start: 0.8681 (t-100) cc_final: 0.7894 (t-100)
REVERT: B  112 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8305 (m-80)
REVERT: B  114 ASP cc_start: 0.9287 (p0) cc_final: 0.8826 (p0)
REVERT: B  201 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7024 (tm-30)
REVERT: B  295 MET cc_start: 0.9011 (mmm) cc_final: 0.8691 (mmm)
REVERT: B  323 ASP cc_start: 0.9046 (p0) cc_final: 0.8734 (p0)
REVERT: B  345 PHE cc_start: 0.9490 (t80) cc_final: 0.9181 (t80)
REVERT: B  346 MET cc_start: 0.9519 (tmm) cc_final: 0.9284 (tmm)
REVERT: B  371 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7491 (mpt180)
REVERT: B  382 MET cc_start: 0.9417 (tpp) cc_final: 0.8994 (tpp)
REVERT: B  455 LEU cc_start: 0.9560 (mp) cc_final: 0.9359 (mt)
  outliers start: 31
  outliers final: 26
  residues processed: 219
  average time/residue: 0.1527
  time to fit residues: 50.9287
Evaluate side-chains
  227 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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  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  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   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  201 GLN
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  403 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   chunk 106 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
B 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.094858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.072227 restraints weight = 22553.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.074757 restraints weight = 11509.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.076432 restraints weight = 7535.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8818  Z= 0.186
  Angle     :  0.730  15.439  11978  Z= 0.361
  Chirality :  0.043   0.205   1388
  Planarity :  0.005   0.065   1458
  Dihedral  :  7.239  75.571   1288
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.98 %
    Favored  : 73.97 %
  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:  1.31 (0.26), residues: 1074
  helix:  1.56 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop : -1.14 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 562 
 HIS   0.020   0.001   HIS B  40 
 PHE   0.044   0.001   PHE A 378 
 TYR   0.040   0.001   TYR A 282 
 ARG   0.001   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
  232 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 204
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8788 (t70) cc_final: 0.8475 (t0)
REVERT: A  114 ASP cc_start: 0.8941 (p0) cc_final: 0.8637 (p0)
REVERT: A  256 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8624 (mm-30)
REVERT: A  332 MET cc_start: 0.8940 (tpp) cc_final: 0.8709 (mmt)
REVERT: A  338 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8792 (mp10)
REVERT: A  349 MET cc_start: 0.8978 (tpt) cc_final: 0.8531 (tpp)
REVERT: A  395 TYR cc_start: 0.6950 (t80) cc_final: 0.6702 (t80)
REVERT: A  501 HIS cc_start: 0.8804 (t70) cc_final: 0.8523 (t-170)
REVERT: A  532 TYR cc_start: 0.7899 (t80) cc_final: 0.7440 (t80)
REVERT: A  539 ASP cc_start: 0.9242 (m-30) cc_final: 0.8906 (m-30)
REVERT: A  562 TRP cc_start: 0.8680 (t-100) cc_final: 0.7888 (t-100)
REVERT: B  112 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8293 (m-80)
REVERT: B  114 ASP cc_start: 0.9276 (p0) cc_final: 0.8866 (p0)
REVERT: B  201 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7036 (tm-30)
REVERT: B  295 MET cc_start: 0.8984 (mmm) cc_final: 0.8693 (mmm)
REVERT: B  323 ASP cc_start: 0.9048 (p0) cc_final: 0.8742 (p0)
REVERT: B  346 MET cc_start: 0.9522 (tmm) cc_final: 0.9297 (tmm)
REVERT: B  371 ARG cc_start: 0.7973 (tpp-160) cc_final: 0.7520 (mpt180)
REVERT: B  382 MET cc_start: 0.9384 (tpp) cc_final: 0.9041 (tpp)
  outliers start: 28
  outliers final: 24
  residues processed: 216
  average time/residue: 0.1533
  time to fit residues: 50.1332
Evaluate side-chains
  223 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
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  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  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   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  201 GLN
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  403 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 99 optimal weight:    0.4980
   chunk 34 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0870
   chunk 66 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 485 ASN
B  40 HIS
B 201 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.095192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.072304 restraints weight = 23014.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.074835 restraints weight = 11693.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.076562 restraints weight = 7655.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.2796

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= 0.180
  Angle     :  0.744  15.451  11978  Z= 0.365
  Chirality :  0.043   0.204   1388
  Planarity :  0.005   0.065   1458
  Dihedral  :  7.160  74.231   1288
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 23.64 %
    Favored  : 73.75 %
  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:  1.54 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop : -1.12 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 562 
 HIS   0.018   0.001   HIS B  40 
 PHE   0.023   0.001   PHE B 573 
 TYR   0.036   0.001   TYR A 282 
 ARG   0.001   0.000   ARG A 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2580.00 seconds
wall clock time: 47 minutes 16.08 seconds (2836.08 seconds total)