Starting phenix.real_space_refine
on Sat Aug 23 02:21:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tpp_41480/08_2025/8tpp_41480.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tpp_41480/08_2025/8tpp_41480.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tpp_41480/08_2025/8tpp_41480.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tpp_41480/08_2025/8tpp_41480.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tpp_41480/08_2025/8tpp_41480.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tpp_41480/08_2025/8tpp_41480.map"
  }
  resolution = 3.64
  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=   0.000 sd=   0.002
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
     Ca      4      9.91       5
     S      38      5.16       5
     C    5968      2.51       5
     N    1524      2.21       5
     O    1582      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  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: 9116
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4556
          Classifications: {'peptide': 584}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 23, 'TRANS': 560}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 191
          Unresolved non-hydrogen angles: 241
          Unresolved non-hydrogen dihedrals: 169
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 6, 'PHE:plan': 4, 'TRP:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 145
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.99, per 1000 atoms: 0.44
  Number of scatterers: 9116
  At special positions: 0
  Unit cell: (86.45, 139.23, 100.1, 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)
     Ca      4     19.99
     S      38     16.00
     O    1582      8.00
     N    1524      7.00
     C    5968      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: 1.01
  Conformation dependent library (CDL) restraints added in 362.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2220

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      74.1% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 31
      No H-bonds generated for 'chain 'A' and resid 29 through 31'
    Processing helix  chain 'A' and resid 32 through 47
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.552A  pdb=" N   PHE A  76 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.728A  pdb=" N   ASP A 107 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
    Processing helix  chain 'A' and resid 126 through 130
    Processing helix  chain 'A' and resid 152 through 164
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.701A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 199
      removed outlier: 3.841A  pdb=" N   ALA A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 217 through 246
    Processing helix  chain 'A' and resid 250 through 254
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.637A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 319
      removed outlier: 3.614A  pdb=" N   PHE A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 358
      Proline residue:  A 341  - end of helix
    Processing helix  chain 'A' and resid 362 through 392
      removed outlier: 5.143A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 408
    Processing helix  chain 'A' and resid 431 through 451
      removed outlier: 3.923A  pdb=" N   ASN A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   THR A 443 " --> pdb=" O   TYR A 439 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A 449 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 465
      removed outlier: 3.658A  pdb=" N   TYR A 457 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 493
    Processing helix  chain 'A' and resid 500 through 518
      removed outlier: 3.766A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 545
      removed outlier: 3.564A  pdb=" N   CYS A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.626A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 560 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA A 578 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN A 585 " --> pdb=" O   TYR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 625
    Processing helix  chain 'A' and resid 630 through 642
    Processing helix  chain 'A' and resid 701 through 715
    Processing helix  chain 'B' and resid 29 through 31
      No H-bonds generated for 'chain 'B' and resid 29 through 31'
    Processing helix  chain 'B' and resid 32 through 47
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.551A  pdb=" N   PHE B  76 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.728A  pdb=" N   ASP B 107 " --> pdb=" O   GLN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 125
    Processing helix  chain 'B' and resid 126 through 130
    Processing helix  chain 'B' and resid 152 through 164
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.700A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 199
      removed outlier: 3.841A  pdb=" N   ALA B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 217 through 246
    Processing helix  chain 'B' and resid 250 through 254
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.637A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 319
      removed outlier: 3.614A  pdb=" N   PHE B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 358
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 362 through 392
      removed outlier: 5.144A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 408
    Processing helix  chain 'B' and resid 431 through 451
      removed outlier: 3.922A  pdb=" N   ASN B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   THR B 443 " --> pdb=" O   TYR B 439 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA B 444 " --> pdb=" O   PHE B 440 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 465
      removed outlier: 3.658A  pdb=" N   TYR B 457 " --> pdb=" O   VAL B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 493
    Processing helix  chain 'B' and resid 500 through 518
      removed outlier: 3.766A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 545
      removed outlier: 3.565A  pdb=" N   CYS B 527 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.625A  pdb=" N   ALA B 564 " --> pdb=" O   PRO B 560 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA B 578 " --> pdb=" O   ILE B 574 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASN B 585 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 625
    Processing helix  chain 'B' and resid 630 through 642
    Processing helix  chain 'B' and resid 701 through 715
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267
      removed outlier: 4.010A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A 267 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 59
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 267
      removed outlier: 4.010A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA B 267 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)

    648 hydrogen bonds defined for protein.
    1902 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2860
        1.34 -     1.46: 2385
        1.46 -     1.58: 4035
        1.58 -     1.70: 0
        1.70 -     1.82: 62
  Bond restraints: 9342
  Sorted by residual:
  bond pdb=" C   ILE B 201 "
       pdb=" N   PRO B 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.28e-02 6.10e+03 2.44e+00
  bond pdb=" C   ILE A 201 "
       pdb=" N   PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.28e-02 6.10e+03 2.31e+00
  bond pdb=" C   ILE A 394 "
       pdb=" N   PRO A 395 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.20e-02 6.94e+03 2.20e+00
  bond pdb=" C   ILE B 394 "
       pdb=" N   PRO B 395 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.20e-02 6.94e+03 2.17e+00
  bond pdb=" CB  GLU B  62 "
       pdb=" CG  GLU B  62 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.11e+00
  ... (remaining 9337 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 12366
        1.36 -     2.72: 266
        2.72 -     4.07: 50
        4.07 -     5.43: 13
        5.43 -     6.79: 11
  Bond angle restraints: 12706
  Sorted by residual:
  angle pdb=" N   THR A 340 "
        pdb=" CA  THR A 340 "
        pdb=" C   THR A 340 "
      ideal   model   delta    sigma   weight residual
     109.81  116.05   -6.24 2.21e+00 2.05e-01 7.98e+00
  angle pdb=" N   THR B 340 "
        pdb=" CA  THR B 340 "
        pdb=" C   THR B 340 "
      ideal   model   delta    sigma   weight residual
     109.81  116.00   -6.19 2.21e+00 2.05e-01 7.85e+00
  angle pdb=" CA  GLU A  62 "
        pdb=" CB  GLU A  62 "
        pdb=" CG  GLU A  62 "
      ideal   model   delta    sigma   weight residual
     114.10  118.87   -4.77 2.00e+00 2.50e-01 5.70e+00
  angle pdb=" CA  GLU B  62 "
        pdb=" CB  GLU B  62 "
        pdb=" CG  GLU B  62 "
      ideal   model   delta    sigma   weight residual
     114.10  118.87   -4.77 2.00e+00 2.50e-01 5.69e+00
  angle pdb=" N   GLU A 264 "
        pdb=" CA  GLU A 264 "
        pdb=" C   GLU A 264 "
      ideal   model   delta    sigma   weight residual
     112.93  109.97    2.96 1.33e+00 5.65e-01 4.94e+00
  ... (remaining 12701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 4668
       17.46 -    34.92: 594
       34.92 -    52.38: 139
       52.38 -    69.84: 23
       69.84 -    87.30: 8
  Dihedral angle restraints: 5432
    sinusoidal: 2026
      harmonic: 3406
  Sorted by residual:
  dihedral pdb=" CG  ARG B 490 "
           pdb=" CD  ARG B 490 "
           pdb=" NE  ARG B 490 "
           pdb=" CZ  ARG B 490 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.09  -44.09     2      1.50e+01 4.44e-03 1.03e+01
  dihedral pdb=" CG  ARG A 490 "
           pdb=" CD  ARG A 490 "
           pdb=" NE  ARG A 490 "
           pdb=" CZ  ARG A 490 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.03  -44.03     2      1.50e+01 4.44e-03 1.03e+01
  dihedral pdb=" CG  ARG B 284 "
           pdb=" CD  ARG B 284 "
           pdb=" NE  ARG B 284 "
           pdb=" CZ  ARG B 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.71  -42.71     2      1.50e+01 4.44e-03 9.81e+00
  ... (remaining 5429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1159
       0.045 -    0.091: 234
       0.091 -    0.136: 49
       0.136 -    0.181: 2
       0.181 -    0.226: 2
  Chirality restraints: 1446
  Sorted by residual:
  chirality pdb=" CB  VAL B 134 "
            pdb=" CA  VAL B 134 "
            pdb=" CG1 VAL B 134 "
            pdb=" CG2 VAL B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CB  VAL A 134 "
            pdb=" CA  VAL A 134 "
            pdb=" CG1 VAL A 134 "
            pdb=" CG2 VAL A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  THR A 340 "
            pdb=" N   THR A 340 "
            pdb=" C   THR A 340 "
            pdb=" CB  THR A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 1443 not shown)

  Planarity restraints: 1592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  62 "   -0.007 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" CD  GLU A  62 "    0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  62 "   -0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  62 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  62 "    0.007 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" CD  GLU B  62 "   -0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  62 "    0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  62 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 201 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO B 202 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 202 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 202 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1589 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1617
        2.76 -     3.30: 8695
        3.30 -     3.83: 15211
        3.83 -     4.37: 15299
        4.37 -     4.90: 28303
  Nonbonded interactions: 69125
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 188 "
            pdb=" OD2 ASP B 539 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OH  TYR A 188 "
            pdb=" OD2 ASP A 539 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OH  TYR B  26 "
            pdb=" O   ALA B  36 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OH  TYR A  26 "
            pdb=" O   ALA A  36 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR B 555 "
            pdb=" O   SER B 557 "
     model   vdw
     2.349 3.040
  ... (remaining 69120 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: 0.02
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:             3.190
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.010
  Find NCS groups from input model:        0.070
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
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      :  0.003   0.032   9342  Z= 0.128
  Angle     :  0.526   6.790  12706  Z= 0.281
  Chirality :  0.038   0.226   1446
  Planarity :  0.004   0.036   1592
  Dihedral  : 16.551  87.300   3212
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 23.92 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.18 (0.26), residues: 1132
  helix:  2.43 (0.18), residues: 800
  sheet: -0.42 (0.82), residues: 44
  loop : -1.19 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 710 
 TYR   0.008   0.001   TYR A 188 
 PHE   0.014   0.001   PHE A 379 
 TRP   0.009   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9342)
  covalent geometry    : angle       0.52646 (12706)
  hydrogen bonds       : bond        0.13660 (  648)
  hydrogen bonds       : angle       5.53900 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.319 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0791
  time to fit residues: 8.8152
Evaluate side-chains
  68 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.3980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 435 ASN
A 698 GLN
B  58 HIS
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 698 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.130309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.104841 restraints weight = 13953.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.106917 restraints weight = 9240.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.108055 restraints weight = 7199.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.109052 restraints weight = 6211.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.109500 restraints weight = 5635.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.0810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9342  Z= 0.127
  Angle     :  0.506   6.823  12706  Z= 0.261
  Chirality :  0.038   0.160   1446
  Planarity :  0.004   0.036   1592
  Dihedral  :  3.542  15.100   1238
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 22.62 %
    Favored  : 75.32 %
  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:  2.71 (0.25), residues: 1132
  helix:  2.80 (0.18), residues: 806
  sheet: -0.10 (0.83), residues: 44
  loop : -1.03 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 710 
 TYR   0.012   0.001   TYR A 188 
 PHE   0.012   0.001   PHE A 379 
 TRP   0.010   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9342)
  covalent geometry    : angle       0.50552 (12706)
  hydrogen bonds       : bond        0.04470 (  648)
  hydrogen bonds       : angle       3.78112 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: A  125 LYS cc_start: 0.7493 (ttmt) cc_final: 0.7223 (tppt)
REVERT: B  125 LYS cc_start: 0.7414 (ttmt) cc_final: 0.7162 (tppt)
  outliers start: 19
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0785
  time to fit residues: 11.3377
Evaluate side-chains
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 102 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 GLN
A 714 GLN
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 ASN
B 633 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.129003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.103546 restraints weight = 13973.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.105567 restraints weight = 9301.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.106901 restraints weight = 7264.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.107560 restraints weight = 6240.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.108003 restraints weight = 5716.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9342  Z= 0.132
  Angle     :  0.505   6.295  12706  Z= 0.259
  Chirality :  0.038   0.144   1446
  Planarity :  0.003   0.034   1592
  Dihedral  :  3.573  14.190   1238
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.73 %
    Favored  : 74.68 %
  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:  2.63 (0.25), residues: 1132
  helix:  2.74 (0.18), residues: 806
  sheet:  0.09 (0.79), residues: 44
  loop : -1.08 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 710 
 TYR   0.010   0.001   TYR A 188 
 PHE   0.013   0.001   PHE A 379 
 TRP   0.010   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9342)
  covalent geometry    : angle       0.50494 (12706)
  hydrogen bonds       : bond        0.04386 (  648)
  hydrogen bonds       : angle       3.55880 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7794 (tm-30)
REVERT: A  125 LYS cc_start: 0.7502 (ttmt) cc_final: 0.7255 (tppt)
REVERT: A  482 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7742 (pm20)
REVERT: B  125 LYS cc_start: 0.7516 (ttmt) cc_final: 0.7261 (tppt)
  outliers start: 24
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0707
  time to fit residues: 10.5714
Evaluate side-chains
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 22 optimal weight:    0.3980
   chunk 7 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 143 HIS
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 714 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.129194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.103794 restraints weight = 14159.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.105884 restraints weight = 9375.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.107067 restraints weight = 7275.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.107992 restraints weight = 6267.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.108371 restraints weight = 5708.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9342  Z= 0.122
  Angle     :  0.490   6.284  12706  Z= 0.252
  Chirality :  0.038   0.144   1446
  Planarity :  0.003   0.034   1592
  Dihedral  :  3.575  14.632   1238
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.05 %
    Favored  : 74.35 %
  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:  2.59 (0.25), residues: 1132
  helix:  2.72 (0.18), residues: 808
  sheet:  0.29 (0.81), residues: 44
  loop : -1.20 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 710 
 TYR   0.010   0.001   TYR A 188 
 PHE   0.013   0.001   PHE A 396 
 TRP   0.010   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9342)
  covalent geometry    : angle       0.49033 (12706)
  hydrogen bonds       : bond        0.04147 (  648)
  hydrogen bonds       : angle       3.39724 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7500 (ttmt) cc_final: 0.7263 (tppt)
REVERT: A  482 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7790 (pm20)
REVERT: B  125 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7281 (tppt)
  outliers start: 24
  outliers final: 18
  residues processed: 92
  average time/residue: 0.0667
  time to fit residues: 9.7648
Evaluate side-chains
  88 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  493 CYS
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0980
   chunk 109 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 143 HIS
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.128552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.103317 restraints weight = 14072.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.105336 restraints weight = 9347.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.106454 restraints weight = 7290.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.107410 restraints weight = 6307.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.107713 restraints weight = 5729.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9342  Z= 0.129
  Angle     :  0.498   6.304  12706  Z= 0.255
  Chirality :  0.038   0.145   1446
  Planarity :  0.003   0.033   1592
  Dihedral  :  3.581  14.575   1238
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 23.48 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.54 (0.25), residues: 1132
  helix:  2.68 (0.18), residues: 808
  sheet:  0.37 (0.83), residues: 44
  loop : -1.26 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 710 
 TYR   0.010   0.001   TYR A 188 
 PHE   0.013   0.001   PHE A 396 
 TRP   0.010   0.001   TRP A 235 
 HIS   0.003   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9342)
  covalent geometry    : angle       0.49750 (12706)
  hydrogen bonds       : bond        0.04209 (  648)
  hydrogen bonds       : angle       3.38773 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7499 (ttmt) cc_final: 0.7270 (tppt)
REVERT: A  482 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7815 (pm20)
REVERT: A  701 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.4962 (mtt)
REVERT: B  125 LYS cc_start: 0.7525 (ttmt) cc_final: 0.7294 (tppt)
  outliers start: 31
  outliers final: 22
  residues processed: 92
  average time/residue: 0.0742
  time to fit residues: 10.7503
Evaluate side-chains
  92 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  701 MET
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 109 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.127813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.102400 restraints weight = 14139.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.104406 restraints weight = 9479.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.105692 restraints weight = 7440.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.106308 restraints weight = 6402.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.106793 restraints weight = 5885.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9342  Z= 0.144
  Angle     :  0.511   6.314  12706  Z= 0.262
  Chirality :  0.038   0.144   1446
  Planarity :  0.003   0.034   1592
  Dihedral  :  3.622  15.315   1238
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.48 %
    Favored  : 72.84 %
  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:  2.48 (0.25), residues: 1132
  helix:  2.64 (0.18), residues: 808
  sheet:  0.53 (0.83), residues: 44
  loop : -1.33 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 710 
 TYR   0.010   0.001   TYR A 188 
 PHE   0.015   0.001   PHE A 396 
 TRP   0.010   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9342)
  covalent geometry    : angle       0.51095 (12706)
  hydrogen bonds       : bond        0.04389 (  648)
  hydrogen bonds       : angle       3.39597 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 72
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7511 (ttmt) cc_final: 0.7276 (tppt)
REVERT: A  482 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7842 (pm20)
REVERT: A  701 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.5025 (mtt)
REVERT: B  125 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7307 (tppt)
  outliers start: 34
  outliers final: 27
  residues processed: 95
  average time/residue: 0.0698
  time to fit residues: 10.6881
Evaluate side-chains
  98 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  701 MET
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  602 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.126977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.101594 restraints weight = 14208.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.103515 restraints weight = 9485.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.104784 restraints weight = 7477.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.105509 restraints weight = 6461.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.105651 restraints weight = 5902.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9342  Z= 0.157
  Angle     :  0.530   6.319  12706  Z= 0.271
  Chirality :  0.039   0.145   1446
  Planarity :  0.004   0.034   1592
  Dihedral  :  3.676  15.806   1238
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 22.62 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.35 (0.25), residues: 1132
  helix:  2.57 (0.18), residues: 810
  sheet:  0.62 (0.85), residues: 44
  loop : -1.53 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 710 
 TYR   0.010   0.001   TYR A 188 
 PHE   0.016   0.001   PHE A 396 
 TRP   0.010   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 9342)
  covalent geometry    : angle       0.52961 (12706)
  hydrogen bonds       : bond        0.04592 (  648)
  hydrogen bonds       : angle       3.42730 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 71
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7292 (tppt)
REVERT: A  263 TRP cc_start: 0.8039 (OUTLIER) cc_final: 0.7354 (p-90)
REVERT: A  482 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7856 (pm20)
  outliers start: 44
  outliers final: 35
  residues processed: 104
  average time/residue: 0.0747
  time to fit residues: 12.1294
Evaluate side-chains
  104 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 67
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  602 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 105 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.127554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.102211 restraints weight = 14146.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.104198 restraints weight = 9464.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.105275 restraints weight = 7433.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.106252 restraints weight = 6450.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.106369 restraints weight = 5858.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9342  Z= 0.131
  Angle     :  0.518   6.276  12706  Z= 0.263
  Chirality :  0.038   0.145   1446
  Planarity :  0.003   0.037   1592
  Dihedral  :  3.672  15.766   1238
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.94 %
    Favored  : 72.51 %
  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:  2.37 (0.25), residues: 1132
  helix:  2.60 (0.18), residues: 810
  sheet:  0.63 (0.85), residues: 44
  loop : -1.56 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 710 
 TYR   0.010   0.001   TYR A 188 
 PHE   0.014   0.001   PHE A 396 
 TRP   0.011   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9342)
  covalent geometry    : angle       0.51788 (12706)
  hydrogen bonds       : bond        0.04349 (  648)
  hydrogen bonds       : angle       3.38143 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 68
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7492 (ttmt) cc_final: 0.7267 (tppt)
REVERT: A  263 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.7358 (p-90)
REVERT: A  482 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7865 (pm20)
REVERT: B  263 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.7294 (p-90)
  outliers start: 42
  outliers final: 34
  residues processed: 100
  average time/residue: 0.0682
  time to fit residues: 11.0502
Evaluate side-chains
  104 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 67
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  263 TRP
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  602 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 114 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.127592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.102309 restraints weight = 14105.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.104294 restraints weight = 9447.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.105426 restraints weight = 7402.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.106346 restraints weight = 6424.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.106347 restraints weight = 5845.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9342  Z= 0.133
  Angle     :  0.517   6.436  12706  Z= 0.263
  Chirality :  0.038   0.152   1446
  Planarity :  0.003   0.038   1592
  Dihedral  :  3.665  15.897   1238
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.73 %
    Favored  : 72.73 %
  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:  2.37 (0.25), residues: 1132
  helix:  2.60 (0.18), residues: 810
  sheet:  0.64 (0.85), residues: 44
  loop : -1.56 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 710 
 TYR   0.010   0.001   TYR A 188 
 PHE   0.014   0.001   PHE B 396 
 TRP   0.011   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9342)
  covalent geometry    : angle       0.51684 (12706)
  hydrogen bonds       : bond        0.04322 (  648)
  hydrogen bonds       : angle       3.37306 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 69
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  125 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7264 (tppt)
REVERT: A  263 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7372 (p-90)
REVERT: A  482 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7875 (pm20)
REVERT: B  263 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.7304 (p-90)
  outliers start: 42
  outliers final: 38
  residues processed: 101
  average time/residue: 0.0662
  time to fit residues: 10.9106
Evaluate side-chains
  109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 68
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  263 TRP
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  602 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.126995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.101691 restraints weight = 14104.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103638 restraints weight = 9421.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.104917 restraints weight = 7409.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.105437 restraints weight = 6383.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.105804 restraints weight = 5915.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9342  Z= 0.153
  Angle     :  0.532   6.489  12706  Z= 0.271
  Chirality :  0.039   0.156   1446
  Planarity :  0.004   0.039   1592
  Dihedral  :  3.690  15.922   1238
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 22.40 %
    Favored  : 72.84 %
  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:  2.31 (0.25), residues: 1132
  helix:  2.55 (0.18), residues: 810
  sheet:  0.62 (0.85), residues: 44
  loop : -1.58 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 710 
 TYR   0.013   0.001   TYR B 383 
 PHE   0.016   0.001   PHE A 396 
 TRP   0.010   0.001   TRP A 235 
 HIS   0.004   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9342)
  covalent geometry    : angle       0.53244 (12706)
  hydrogen bonds       : bond        0.04516 (  648)
  hydrogen bonds       : angle       3.40713 ( 1902)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 71
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7146 (mp0) cc_final: 0.6705 (mp0)
REVERT: A  125 LYS cc_start: 0.7492 (ttmt) cc_final: 0.7267 (tppt)
REVERT: A  263 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.7375 (p-90)
REVERT: A  482 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7876 (pm20)
REVERT: B  263 TRP cc_start: 0.7991 (OUTLIER) cc_final: 0.7314 (p-90)
  outliers start: 44
  outliers final: 39
  residues processed: 105
  average time/residue: 0.0702
  time to fit residues: 11.6959
Evaluate side-chains
  109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 67
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  153 HIS
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  516 MET
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  153 HIS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  263 TRP
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  575 THR
Chi-restraints excluded: chain B residue  602 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain B residue  705 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 77 optimal weight:    0.1980
   chunk 87 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 105 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 359 ASN
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.128266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.103054 restraints weight = 13934.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.105082 restraints weight = 9352.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.106261 restraints weight = 7315.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.107196 restraints weight = 6309.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.107197 restraints weight = 5744.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9342  Z= 0.119
  Angle     :  0.516   6.440  12706  Z= 0.261
  Chirality :  0.038   0.152   1446
  Planarity :  0.003   0.039   1592
  Dihedral  :  3.668  15.835   1238
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 23.05 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.41 (0.25), residues: 1132
  helix:  2.63 (0.17), residues: 810
  sheet:  0.60 (0.85), residues: 44
  loop : -1.54 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 710 
 TYR   0.013   0.001   TYR B 383 
 PHE   0.013   0.001   PHE B 379 
 TRP   0.012   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9342)
  covalent geometry    : angle       0.51578 (12706)
  hydrogen bonds       : bond        0.04172 (  648)
  hydrogen bonds       : angle       3.36458 ( 1902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1439.25 seconds
wall clock time: 25 minutes 41.90 seconds (1541.90 seconds total)