Starting phenix.real_space_refine
on Fri Aug 22 23:28:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zl4_60218/08_2025/8zl4_60218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zl4_60218/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zl4_60218/08_2025/8zl4_60218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zl4_60218/08_2025/8zl4_60218.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zl4_60218/08_2025/8zl4_60218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zl4_60218/08_2025/8zl4_60218.map"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.64, per 1000 atoms: 0.19
  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: 0.76
  Conformation dependent library (CDL) restraints added in 208.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.16
  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: 0.94

  Time building geometry restraints manager: 0.91 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: 0.01
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:             0.890
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.640
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.760
-------------------------------------------------------------------------------
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= 0.271
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG B 137 
 TYR   0.029   0.002   TYR B 282 
 PHE   0.028   0.002   PHE A 378 
 TRP   0.016   0.002   TRP A  78 
 HIS   0.007   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 8818)
  covalent geometry    : angle       0.82428 (11978)
  hydrogen bonds       : bond        0.15381 (  540)
  hydrogen bonds       : angle       5.86334 ( 1617)

*********************** 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  : 0.305 
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: 0.0473
  time to fit residues: 16.9344
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  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3398 r_free = 0.3398 target = 0.093031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.069679 restraints weight = 23254.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.072200 restraints weight = 11860.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.073619 restraints weight = 7800.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.074810 restraints weight = 6171.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.075416 restraints weight = 5182.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1459

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= 0.138
  Angle     :  0.659   8.015  11978  Z= 0.347
  Chirality :  0.043   0.201   1388
  Planarity :  0.005   0.064   1458
  Dihedral  :  9.013 108.385   1288
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 10.24 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.26), residues: 1074
  helix:  1.56 (0.18), residues: 802
  sheet:  None (None), residues: 0
  loop : -1.37 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 325 
 TYR   0.036   0.001   TYR B 282 
 PHE   0.033   0.002   PHE A 378 
 TRP   0.013   0.001   TRP B 292 
 HIS   0.006   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8818)
  covalent geometry    : angle       0.65889 (11978)
  hydrogen bonds       : bond        0.04941 (  540)
  hydrogen bonds       : angle       4.50740 ( 1617)

*********************** 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
  239 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 221
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8720 (t70) cc_final: 0.8365 (t0)
REVERT: A  114 ASP cc_start: 0.8880 (p0) cc_final: 0.8509 (p0)
REVERT: A  135 HIS cc_start: 0.8501 (p-80) cc_final: 0.8059 (p-80)
REVERT: A  159 MET cc_start: 0.9152 (tpp) cc_final: 0.8813 (mmm)
REVERT: A  166 MET cc_start: 0.8839 (ttm) cc_final: 0.8634 (ttm)
REVERT: A  256 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8604 (mm-30)
REVERT: A  395 TYR cc_start: 0.6909 (t80) cc_final: 0.6655 (t80)
REVERT: A  532 TYR cc_start: 0.7441 (t80) cc_final: 0.6946 (t80)
REVERT: A  562 TRP cc_start: 0.8608 (t-100) cc_final: 0.8036 (t-100)
REVERT: B   68 MET cc_start: 0.9063 (ttt) cc_final: 0.8671 (ttp)
REVERT: B  127 LEU cc_start: 0.9735 (mm) cc_final: 0.9482 (mm)
REVERT: B  201 GLN cc_start: 0.7605 (tm-30) cc_final: 0.6862 (tm-30)
REVERT: B  295 MET cc_start: 0.8997 (tpp) cc_final: 0.8783 (mmm)
REVERT: B  323 ASP cc_start: 0.9028 (p0) cc_final: 0.8754 (p0)
REVERT: B  382 MET cc_start: 0.9289 (tpp) cc_final: 0.8952 (tpp)
  outliers start: 18
  outliers final: 11
  residues processed: 228
  average time/residue: 0.0475
  time to fit residues: 16.9147
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 190
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 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  490 VAL
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
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 6 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 102 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.8788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.092055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.069324 restraints weight = 22852.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.071818 restraints weight = 11723.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.073517 restraints weight = 7740.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.074602 restraints weight = 5910.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.075286 restraints weight = 4984.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8818  Z= 0.148
  Angle     :  0.639   8.141  11978  Z= 0.337
  Chirality :  0.042   0.195   1388
  Planarity :  0.005   0.061   1458
  Dihedral  :  8.190 103.170   1288
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.49 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.26), residues: 1074
  helix:  1.59 (0.18), residues: 802
  sheet:  None (None), residues: 0
  loop : -1.36 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 137 
 TYR   0.045   0.002   TYR A 282 
 PHE   0.024   0.001   PHE A 251 
 TRP   0.010   0.001   TRP B 292 
 HIS   0.009   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8818)
  covalent geometry    : angle       0.63900 (11978)
  hydrogen bonds       : bond        0.04676 (  540)
  hydrogen bonds       : angle       4.45537 ( 1617)

*********************** 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
  228 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 200
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8771 (t70) cc_final: 0.8423 (t0)
REVERT: A  114 ASP cc_start: 0.8933 (p0) cc_final: 0.8574 (p0)
REVERT: A  159 MET cc_start: 0.9165 (tpp) cc_final: 0.8931 (mmm)
REVERT: A  256 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8622 (mm-30)
REVERT: A  295 MET cc_start: 0.8361 (mtt) cc_final: 0.8026 (mtt)
REVERT: A  340 MET cc_start: 0.8708 (ttm) cc_final: 0.8472 (ttm)
REVERT: A  395 TYR cc_start: 0.6938 (t80) cc_final: 0.6697 (t80)
REVERT: A  532 TYR cc_start: 0.7660 (t80) cc_final: 0.7380 (t80)
REVERT: A  562 TRP cc_start: 0.8654 (t-100) cc_final: 0.8010 (t-100)
REVERT: B   81 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8289 (tm-30)
REVERT: B  112 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8300 (m-80)
REVERT: B  201 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: B  295 MET cc_start: 0.9035 (tpp) cc_final: 0.8801 (mmm)
REVERT: B  323 ASP cc_start: 0.9040 (p0) cc_final: 0.8752 (p0)
REVERT: B  371 ARG cc_start: 0.8125 (tpp-160) cc_final: 0.7617 (mpt180)
REVERT: B  382 MET cc_start: 0.9289 (tpp) cc_final: 0.9049 (tpp)
REVERT: B  392 PHE cc_start: 0.8452 (p90) cc_final: 0.8243 (p90)
  outliers start: 28
  outliers final: 20
  residues processed: 213
  average time/residue: 0.0486
  time to fit residues: 16.0404
Evaluate side-chains
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 190
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  249 LEU
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 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  490 VAL
Chi-restraints excluded: chain B residue  539 ASP
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 36 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    3.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.090060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.067139 restraints weight = 23715.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.069514 restraints weight = 12215.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.071159 restraints weight = 8105.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.072003 restraints weight = 6232.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.072872 restraints weight = 5359.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8818  Z= 0.218
  Angle     :  0.680   8.359  11978  Z= 0.359
  Chirality :  0.045   0.224   1388
  Planarity :  0.005   0.064   1458
  Dihedral  :  7.889  92.291   1288
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 16.23 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.26), residues: 1074
  helix:  1.53 (0.18), residues: 798
  sheet:  None (None), residues: 0
  loop : -1.31 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 258 
 TYR   0.035   0.002   TYR A 282 
 PHE   0.022   0.002   PHE A 251 
 TRP   0.009   0.001   TRP B 292 
 HIS   0.006   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 8818)
  covalent geometry    : angle       0.68040 (11978)
  hydrogen bonds       : bond        0.05039 (  540)
  hydrogen bonds       : angle       4.60241 ( 1617)

*********************** 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
  224 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 189
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8796 (t70) cc_final: 0.8380 (t0)
REVERT: A  114 ASP cc_start: 0.8992 (p0) cc_final: 0.8657 (p0)
REVERT: A  118 MET cc_start: 0.9139 (ttm) cc_final: 0.8882 (ttm)
REVERT: A  256 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8638 (mm-30)
REVERT: A  332 MET cc_start: 0.8915 (tpp) cc_final: 0.8609 (mmt)
REVERT: A  372 ASN cc_start: 0.8728 (m110) cc_final: 0.8461 (m-40)
REVERT: A  395 TYR cc_start: 0.6997 (t80) cc_final: 0.6711 (t80)
REVERT: A  532 TYR cc_start: 0.7740 (t80) cc_final: 0.7376 (t80)
REVERT: A  562 TRP cc_start: 0.8658 (t-100) cc_final: 0.8018 (t-100)
REVERT: B   81 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8478 (tm-30)
REVERT: B  112 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8318 (m-80)
REVERT: B  114 ASP cc_start: 0.9191 (p0) cc_final: 0.8964 (p0)
REVERT: B  201 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: B  295 MET cc_start: 0.9090 (tpp) cc_final: 0.8734 (mmm)
REVERT: B  323 ASP cc_start: 0.9041 (p0) cc_final: 0.8745 (p0)
REVERT: B  371 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.7582 (mpt180)
REVERT: B  382 MET cc_start: 0.9349 (tpp) cc_final: 0.9074 (tpp)
  outliers start: 35
  outliers final: 29
  residues processed: 202
  average time/residue: 0.0495
  time to fit residues: 15.5312
Evaluate side-chains
  214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  228 LEU
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   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  112 PHE
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  490 VAL
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 21 optimal weight:    9.9990
   chunk 101 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0670
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.1522

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.093591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.071199 restraints weight = 22664.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.073699 restraints weight = 11434.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.075428 restraints weight = 7468.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.076366 restraints weight = 5653.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.077223 restraints weight = 4795.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8818  Z= 0.128
  Angle     :  0.648  12.558  11978  Z= 0.334
  Chirality :  0.042   0.191   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.554  79.881   1288
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.17 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.26), residues: 1074
  helix:  1.60 (0.18), residues: 804
  sheet:  None (None), residues: 0
  loop : -1.40 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 353 
 TYR   0.042   0.001   TYR A 282 
 PHE   0.022   0.001   PHE A 287 
 TRP   0.010   0.001   TRP B 562 
 HIS   0.003   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8818)
  covalent geometry    : angle       0.64789 (11978)
  hydrogen bonds       : bond        0.04316 (  540)
  hydrogen bonds       : angle       4.31072 ( 1617)

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

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 208
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8772 (t70) cc_final: 0.8420 (t0)
REVERT: A  114 ASP cc_start: 0.8887 (p0) cc_final: 0.8536 (p0)
REVERT: A  159 MET cc_start: 0.9139 (tpp) cc_final: 0.8917 (mmm)
REVERT: A  224 LEU cc_start: 0.9545 (mt) cc_final: 0.9252 (mt)
REVERT: A  256 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8632 (mm-30)
REVERT: A  332 MET cc_start: 0.8929 (tpp) cc_final: 0.8614 (mmt)
REVERT: A  349 MET cc_start: 0.8958 (tpt) cc_final: 0.8396 (tpp)
REVERT: A  372 ASN cc_start: 0.8764 (m110) cc_final: 0.8397 (m-40)
REVERT: A  382 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8770 (mtm)
REVERT: A  395 TYR cc_start: 0.6933 (t80) cc_final: 0.6693 (t80)
REVERT: A  501 HIS cc_start: 0.8837 (t70) cc_final: 0.8501 (t-170)
REVERT: A  532 TYR cc_start: 0.7764 (t80) cc_final: 0.7352 (t80)
REVERT: A  562 TRP cc_start: 0.8650 (t-100) cc_final: 0.7960 (t-100)
REVERT: B   81 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8578 (tm-30)
REVERT: B  112 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8236 (m-80)
REVERT: B  201 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7185 (tm-30)
REVERT: B  323 ASP cc_start: 0.9021 (p0) cc_final: 0.8716 (p0)
REVERT: B  371 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7560 (mpt180)
REVERT: B  382 MET cc_start: 0.9351 (tpp) cc_final: 0.9050 (tpp)
  outliers start: 30
  outliers final: 25
  residues processed: 217
  average time/residue: 0.0481
  time to fit residues: 16.3875
Evaluate side-chains
  218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  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  243 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  491 LEU
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  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  490 VAL
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 89 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 106 optimal weight:   10.0000
   chunk 92 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.093616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.070747 restraints weight = 22611.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.073266 restraints weight = 11534.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.074981 restraints weight = 7593.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.075974 restraints weight = 5782.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.076739 restraints weight = 4896.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8818  Z= 0.146
  Angle     :  0.657  13.660  11978  Z= 0.337
  Chirality :  0.042   0.178   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.468  77.470   1288
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.83 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.26), residues: 1074
  helix:  1.65 (0.18), residues: 800
  sheet:  None (None), residues: 0
  loop : -1.32 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 353 
 TYR   0.040   0.001   TYR A 282 
 PHE   0.018   0.001   PHE B 251 
 TRP   0.009   0.001   TRP B 562 
 HIS   0.004   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8818)
  covalent geometry    : angle       0.65675 (11978)
  hydrogen bonds       : bond        0.04323 (  540)
  hydrogen bonds       : angle       4.30332 ( 1617)

*********************** 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
  229 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 194
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8779 (t70) cc_final: 0.8351 (t0)
REVERT: A  114 ASP cc_start: 0.8886 (p0) cc_final: 0.8619 (p0)
REVERT: A  159 MET cc_start: 0.9143 (tpp) cc_final: 0.8931 (mmm)
REVERT: A  224 LEU cc_start: 0.9539 (mt) cc_final: 0.9273 (mt)
REVERT: A  256 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8625 (mm-30)
REVERT: A  332 MET cc_start: 0.8922 (tpp) cc_final: 0.8588 (mmt)
REVERT: A  382 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8413 (mtm)
REVERT: A  395 TYR cc_start: 0.6962 (t80) cc_final: 0.6715 (t80)
REVERT: A  532 TYR cc_start: 0.7781 (t80) cc_final: 0.7362 (t80)
REVERT: A  539 ASP cc_start: 0.9196 (m-30) cc_final: 0.8983 (m-30)
REVERT: A  562 TRP cc_start: 0.8663 (t-100) cc_final: 0.7954 (t-100)
REVERT: B  112 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8296 (m-80)
REVERT: B  201 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7215 (tm-30)
REVERT: B  323 ASP cc_start: 0.9031 (p0) cc_final: 0.8725 (p0)
REVERT: B  371 ARG cc_start: 0.7977 (tpp-160) cc_final: 0.7531 (mpt180)
REVERT: B  382 MET cc_start: 0.9374 (tpp) cc_final: 0.9054 (tpp)
  outliers start: 35
  outliers final: 26
  residues processed: 209
  average time/residue: 0.0497
  time to fit residues: 16.1867
Evaluate side-chains
  217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
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  169 SER
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  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  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  490 VAL
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 68 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 90 optimal weight:    0.0670
   chunk 25 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.4126

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

Flipped N/Q/H residues before XYZ refinement:
A 144 GLN
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.093907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.071274 restraints weight = 22523.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.073729 restraints weight = 11401.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.075460 restraints weight = 7505.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.076569 restraints weight = 5699.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.077317 restraints weight = 4782.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8818  Z= 0.134
  Angle     :  0.676  14.305  11978  Z= 0.346
  Chirality :  0.043   0.213   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.418  77.610   1288
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.93 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1074
  helix:  1.64 (0.19), residues: 800
  sheet:  None (None), residues: 0
  loop : -1.32 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 137 
 TYR   0.041   0.001   TYR A 282 
 PHE   0.025   0.001   PHE B 345 
 TRP   0.009   0.001   TRP B 562 
 HIS   0.006   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8818)
  covalent geometry    : angle       0.67595 (11978)
  hydrogen bonds       : bond        0.04216 (  540)
  hydrogen bonds       : angle       4.24669 ( 1617)

*********************** 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
  231 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 199
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8761 (t70) cc_final: 0.8498 (t0)
REVERT: A  114 ASP cc_start: 0.8899 (p0) cc_final: 0.8605 (p0)
REVERT: A  159 MET cc_start: 0.9129 (tpp) cc_final: 0.8918 (mmm)
REVERT: A  224 LEU cc_start: 0.9544 (mt) cc_final: 0.9306 (mt)
REVERT: A  256 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8611 (mm-30)
REVERT: A  332 MET cc_start: 0.8964 (tpp) cc_final: 0.8741 (mmt)
REVERT: A  382 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8237 (mpp)
REVERT: A  395 TYR cc_start: 0.6903 (t80) cc_final: 0.6659 (t80)
REVERT: A  501 HIS cc_start: 0.8870 (t70) cc_final: 0.8505 (t-170)
REVERT: A  532 TYR cc_start: 0.7806 (t80) cc_final: 0.7383 (t80)
REVERT: A  562 TRP cc_start: 0.8667 (t-100) cc_final: 0.7932 (t-100)
REVERT: B   37 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.9015 (m-80)
REVERT: B   81 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: B  112 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8292 (m-80)
REVERT: B  201 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7236 (tm-30)
REVERT: B  323 ASP cc_start: 0.9024 (p0) cc_final: 0.8713 (p0)
REVERT: B  371 ARG cc_start: 0.7987 (tpp-160) cc_final: 0.7550 (mpt180)
REVERT: B  382 MET cc_start: 0.9390 (tpp) cc_final: 0.9043 (tpp)
  outliers start: 32
  outliers final: 26
  residues processed: 215
  average time/residue: 0.0624
  time to fit residues: 20.7360
Evaluate side-chains
  220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 191
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  169 SER
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  382 MET
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  518 HIS
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain B residue   37 PHE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  475 THR
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  490 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 27 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 97 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.093347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.070419 restraints weight = 22536.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.072887 restraints weight = 11522.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.074323 restraints weight = 7623.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.075627 restraints weight = 5954.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.076331 restraints weight = 4974.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8818  Z= 0.135
  Angle     :  0.676  14.471  11978  Z= 0.344
  Chirality :  0.043   0.204   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.355  77.437   1288
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 19.93 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.26), residues: 1074
  helix:  1.64 (0.19), residues: 800
  sheet:  None (None), residues: 0
  loop : -1.35 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 137 
 TYR   0.044   0.001   TYR A 282 
 PHE   0.032   0.001   PHE B 345 
 TRP   0.010   0.001   TRP B 562 
 HIS   0.006   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8818)
  covalent geometry    : angle       0.67647 (11978)
  hydrogen bonds       : bond        0.04124 (  540)
  hydrogen bonds       : angle       4.21519 ( 1617)

*********************** 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
  237 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 201
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8787 (t70) cc_final: 0.8460 (t0)
REVERT: A  114 ASP cc_start: 0.8931 (p0) cc_final: 0.8644 (p0)
REVERT: A  159 MET cc_start: 0.9119 (tpp) cc_final: 0.8912 (mmm)
REVERT: A  224 LEU cc_start: 0.9545 (mt) cc_final: 0.9308 (mt)
REVERT: A  256 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8611 (mm-30)
REVERT: A  332 MET cc_start: 0.8964 (tpp) cc_final: 0.8715 (mmt)
REVERT: A  382 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8185 (mpp)
REVERT: A  395 TYR cc_start: 0.6948 (t80) cc_final: 0.6678 (t80)
REVERT: A  532 TYR cc_start: 0.7875 (t80) cc_final: 0.7426 (t80)
REVERT: A  539 ASP cc_start: 0.9198 (m-30) cc_final: 0.8979 (m-30)
REVERT: A  562 TRP cc_start: 0.8673 (t-100) cc_final: 0.7915 (t-100)
REVERT: B   37 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.9009 (m-80)
REVERT: B  112 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8296 (m-80)
REVERT: B  114 ASP cc_start: 0.9286 (p0) cc_final: 0.8841 (p0)
REVERT: B  201 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7266 (tm-30)
REVERT: B  323 ASP cc_start: 0.9033 (p0) cc_final: 0.8725 (p0)
REVERT: B  371 ARG cc_start: 0.8008 (tpp-160) cc_final: 0.7496 (mpt180)
REVERT: B  382 MET cc_start: 0.9395 (tpp) cc_final: 0.9013 (tpp)
  outliers start: 36
  outliers final: 31
  residues processed: 217
  average time/residue: 0.0674
  time to fit residues: 22.6238
Evaluate side-chains
  225 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   54 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  169 SER
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  491 LEU
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  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  490 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 80 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  40 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.095361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.072831 restraints weight = 22341.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.075351 restraints weight = 11297.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.077106 restraints weight = 7374.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.078042 restraints weight = 5576.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.078883 restraints weight = 4717.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8818  Z= 0.131
  Angle     :  0.740  18.231  11978  Z= 0.362
  Chirality :  0.043   0.244   1388
  Planarity :  0.005   0.066   1458
  Dihedral  :  7.274  76.722   1288
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.13 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1074
  helix:  1.64 (0.18), residues: 798
  sheet:  None (None), residues: 0
  loop : -1.33 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 137 
 TYR   0.044   0.001   TYR A 282 
 PHE   0.036   0.001   PHE B 345 
 TRP   0.010   0.001   TRP B 562 
 HIS   0.023   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8818)
  covalent geometry    : angle       0.73961 (11978)
  hydrogen bonds       : bond        0.03985 (  540)
  hydrogen bonds       : angle       4.18947 ( 1617)

*********************** 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
  232 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 203
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8771 (t70) cc_final: 0.8451 (t0)
REVERT: A  114 ASP cc_start: 0.8917 (p0) cc_final: 0.8635 (p0)
REVERT: A  224 LEU cc_start: 0.9533 (mt) cc_final: 0.9279 (mt)
REVERT: A  256 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8573 (mm-30)
REVERT: A  266 MET cc_start: 0.7766 (ttm) cc_final: 0.7379 (ttm)
REVERT: A  349 MET cc_start: 0.8946 (tpt) cc_final: 0.8446 (tpp)
REVERT: A  395 TYR cc_start: 0.6895 (t80) cc_final: 0.6637 (t80)
REVERT: A  501 HIS cc_start: 0.8804 (t70) cc_final: 0.8538 (t-170)
REVERT: A  532 TYR cc_start: 0.7879 (t80) cc_final: 0.7456 (t80)
REVERT: A  539 ASP cc_start: 0.9209 (m-30) cc_final: 0.8990 (m-30)
REVERT: A  562 TRP cc_start: 0.8671 (t-100) cc_final: 0.7904 (t-100)
REVERT: B   37 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.9068 (m-80)
REVERT: B  112 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8267 (m-80)
REVERT: B  114 ASP cc_start: 0.9285 (p0) cc_final: 0.8883 (p0)
REVERT: B  295 MET cc_start: 0.8821 (mmm) cc_final: 0.8154 (mmm)
REVERT: B  323 ASP cc_start: 0.9020 (p0) cc_final: 0.8718 (p0)
REVERT: B  371 ARG cc_start: 0.7992 (tpp-160) cc_final: 0.7484 (mpt180)
REVERT: B  382 MET cc_start: 0.9389 (tpp) cc_final: 0.9003 (tpp)
  outliers start: 29
  outliers final: 25
  residues processed: 216
  average time/residue: 0.0682
  time to fit residues: 22.9410
Evaluate side-chains
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 194
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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  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  243 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  272 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  290 LEU
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  490 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 23 optimal weight:    0.1980
   chunk 98 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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
B 201 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.073647 restraints weight = 22016.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.076181 restraints weight = 11052.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.077895 restraints weight = 7204.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.078813 restraints weight = 5475.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.079695 restraints weight = 4661.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   8818  Z= 0.135
  Angle     :  0.761  16.660  11978  Z= 0.371
  Chirality :  0.044   0.363   1388
  Planarity :  0.005   0.065   1458
  Dihedral  :  7.221  75.203   1288
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.11 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1074
  helix:  1.56 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop : -1.28 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 137 
 TYR   0.044   0.001   TYR A 282 
 PHE   0.034   0.001   PHE B 345 
 TRP   0.010   0.001   TRP B 562 
 HIS   0.015   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8818)
  covalent geometry    : angle       0.76128 (11978)
  hydrogen bonds       : bond        0.03919 (  540)
  hydrogen bonds       : angle       4.25662 ( 1617)

********************** 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
  231 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.8759 (t70) cc_final: 0.8448 (t0)
REVERT: A  114 ASP cc_start: 0.8904 (p0) cc_final: 0.8619 (p0)
REVERT: A  224 LEU cc_start: 0.9543 (mt) cc_final: 0.9259 (mt)
REVERT: A  256 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8551 (mm-30)
REVERT: A  266 MET cc_start: 0.7796 (ttm) cc_final: 0.7434 (ttm)
REVERT: A  349 MET cc_start: 0.8953 (tpt) cc_final: 0.8454 (tpp)
REVERT: A  382 MET cc_start: 0.8842 (mtm) cc_final: 0.8560 (mpp)
REVERT: A  395 TYR cc_start: 0.6886 (t80) cc_final: 0.6651 (t80)
REVERT: A  501 HIS cc_start: 0.8821 (t70) cc_final: 0.8557 (t-170)
REVERT: A  532 TYR cc_start: 0.7912 (t80) cc_final: 0.7492 (t80)
REVERT: A  539 ASP cc_start: 0.9206 (m-30) cc_final: 0.8994 (m-30)
REVERT: A  562 TRP cc_start: 0.8652 (t-100) cc_final: 0.7864 (t-100)
REVERT: B  112 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8239 (m-80)
REVERT: B  114 ASP cc_start: 0.9285 (p0) cc_final: 0.8965 (p0)
REVERT: B  201 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7335 (pp30)
REVERT: B  295 MET cc_start: 0.8813 (mmm) cc_final: 0.8196 (mmm)
REVERT: B  323 ASP cc_start: 0.9026 (p0) cc_final: 0.8725 (p0)
REVERT: B  371 ARG cc_start: 0.8008 (tpp-160) cc_final: 0.7487 (mpt180)
REVERT: B  382 MET cc_start: 0.9316 (tpp) cc_final: 0.9031 (tpp)
  outliers start: 28
  outliers final: 24
  residues processed: 217
  average time/residue: 0.0662
  time to fit residues: 22.4165
Evaluate side-chains
  224 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 198
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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  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  481 VAL
Chi-restraints excluded: chain B residue  490 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 49 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 97 optimal weight:    0.3980
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0070
   chunk 22 optimal weight:    6.9990
   overall best weight:    0.8802

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.095430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.072615 restraints weight = 22272.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.075162 restraints weight = 11252.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.076888 restraints weight = 7342.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.077954 restraints weight = 5579.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.078731 restraints weight = 4702.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.186   8818  Z= 0.269
  Angle     :  1.270  59.199  11978  Z= 0.740
  Chirality :  0.047   0.525   1388
  Planarity :  0.007   0.162   1458
  Dihedral  :  7.234  75.198   1288
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.33 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.26), residues: 1074
  helix:  1.54 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop : -1.28 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 137 
 TYR   0.041   0.001   TYR A 282 
 PHE   0.033   0.001   PHE B 345 
 TRP   0.009   0.001   TRP B 562 
 HIS   0.194   0.008   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 8818)
  covalent geometry    : angle       1.26973 (11978)
  hydrogen bonds       : bond        0.03950 (  540)
  hydrogen bonds       : angle       4.25750 ( 1617)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1321.80 seconds
wall clock time: 23 minutes 36.73 seconds (1416.73 seconds total)