Starting phenix.real_space_refine
on Fri Aug  7 07:43:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t3l_41005/08_2026/8t3l_41005_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t3l_41005/08_2026/8t3l_41005.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t3l_41005/08_2026/8t3l_41005.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t3l_41005/08_2026/8t3l_41005.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t3l_41005/08_2026/8t3l_41005_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t3l_41005/08_2026/8t3l_41005_trim.cif"
  }
  resolution = 3.6
  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=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      70      5.16       5
     Na      2      4.78       5
     C    6715      2.51       5
     N    1522      2.21       5
     O    1753      1.98       5
     H   10056      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 20122
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 5059
          Classifications: {'peptide': 303}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 296}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 5078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 5078
          Classifications: {'peptide': 305}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 298}
    Chain: "B"
      Number of atoms: 4899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 4899
          Classifications: {'peptide': 294}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 287}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 4944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 4944
          Classifications: {'peptide': 295}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 288}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 46
          Unusual residues: {' NA': 1, '8IJ': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "D"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 45
          Unusual residues: {'8IJ': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 26
          Unusual residues: {' NA': 1, 'NKN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'NKN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.72, per 1000 atoms: 0.18
  Number of scatterers: 20122
  At special positions: 0
  Unit cell: (112.725, 112.725, 81.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      70     16.00
     P       4     15.00
     Na      2     11.00
     O    1753      8.00
     N    1522      7.00
     C    6715      6.00
     H   10056      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 523.4 milliseconds
  

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2288

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 0 sheets defined
      81.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 394 through 402
    Processing helix  chain 'A' and resid 410 through 414
      removed outlier: 3.711A  pdb=" N   LEU A 413 " --> pdb=" O   HIS A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 429
    Processing helix  chain 'A' and resid 429 through 454
      removed outlier: 3.555A  pdb=" N   TYR A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 500
    Processing helix  chain 'A' and resid 504 through 508
      removed outlier: 4.072A  pdb=" N   PHE A 507 " --> pdb=" O   LYS A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 532
    Processing helix  chain 'A' and resid 536 through 551
    Processing helix  chain 'A' and resid 552 through 557
    Processing helix  chain 'A' and resid 559 through 599
      removed outlier: 3.873A  pdb=" N   LEU A 577 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   CYS A 578 " --> pdb=" O   LEU A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 639
    Processing helix  chain 'A' and resid 655 through 671
    Processing helix  chain 'A' and resid 673 through 689
    Processing helix  chain 'A' and resid 689 through 711
    Processing helix  chain 'D' and resid 394 through 401
    Processing helix  chain 'D' and resid 411 through 414
    Processing helix  chain 'D' and resid 415 through 429
    Processing helix  chain 'D' and resid 429 through 454
    Processing helix  chain 'D' and resid 468 through 500
    Processing helix  chain 'D' and resid 510 through 532
    Processing helix  chain 'D' and resid 536 through 551
    Processing helix  chain 'D' and resid 552 through 557
      removed outlier: 3.974A  pdb=" N   ARG D 557 " --> pdb=" O   TYR D 554 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 559 through 599
      removed outlier: 4.062A  pdb=" N   LEU D 577 " --> pdb=" O   ILE D 573 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   CYS D 578 " --> pdb=" O   LEU D 574 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 629 through 642
      removed outlier: 4.056A  pdb=" N   PHE D 640 " --> pdb=" O   GLU D 636 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   THR D 641 " --> pdb=" O   LEU D 637 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ILE D 642 " --> pdb=" O   PHE D 638 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 655 through 670
    Processing helix  chain 'D' and resid 673 through 689
    Processing helix  chain 'D' and resid 689 through 711
    Processing helix  chain 'B' and resid 394 through 402
    Processing helix  chain 'B' and resid 411 through 414
    Processing helix  chain 'B' and resid 415 through 429
    Processing helix  chain 'B' and resid 429 through 454
    Processing helix  chain 'B' and resid 468 through 500
    Processing helix  chain 'B' and resid 510 through 531
    Processing helix  chain 'B' and resid 536 through 551
    Processing helix  chain 'B' and resid 552 through 557
      removed outlier: 3.999A  pdb=" N   ARG B 557 " --> pdb=" O   TYR B 554 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 575
    Processing helix  chain 'B' and resid 577 through 599
      removed outlier: 3.803A  pdb=" N   VAL B 583 " --> pdb=" O   ARG B 579 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TYR B 584 " --> pdb=" O   PHE B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 640
      removed outlier: 4.021A  pdb=" N   PHE B 640 " --> pdb=" O   GLU B 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 641 through 643
      No H-bonds generated for 'chain 'B' and resid 641 through 643'
    Processing helix  chain 'B' and resid 655 through 682
      removed outlier: 3.541A  pdb=" N   PHE B 659 " --> pdb=" O   PHE B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 712
      removed outlier: 3.679A  pdb=" N   LYS B 694 " --> pdb=" O   ALA B 690 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 394 through 401
    Processing helix  chain 'C' and resid 408 through 413
      removed outlier: 3.654A  pdb=" N   LEU C 413 " --> pdb=" O   ARG C 409 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 415 through 429
    Processing helix  chain 'C' and resid 429 through 454
    Processing helix  chain 'C' and resid 468 through 499
    Processing helix  chain 'C' and resid 510 through 532
    Processing helix  chain 'C' and resid 536 through 552
    Processing helix  chain 'C' and resid 553 through 557
      removed outlier: 3.731A  pdb=" N   ARG C 557 " --> pdb=" O   TYR C 554 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 599
      removed outlier: 4.949A  pdb=" N   LEU C 577 " --> pdb=" O   ILE C 573 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   CYS C 578 " --> pdb=" O   LEU C 574 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ARG C 579 " --> pdb=" O   ARG C 575 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 602 through 628
    Processing helix  chain 'C' and resid 629 through 639
    Processing helix  chain 'C' and resid 655 through 686
      removed outlier: 4.766A  pdb=" N   MET C 682 " --> pdb=" O   LEU C 678 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 687 through 711
      removed outlier: 4.383A  pdb=" N   GLN C 691 " --> pdb=" O   ASN C 687 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LYS C 694 " --> pdb=" O   ALA C 690 " (cutoff:3.500A)

    740 hydrogen bonds defined for protein.
    2181 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: 4.49

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10038
        1.03 -     1.23: 80
        1.23 -     1.42: 4413
        1.42 -     1.62: 5706
        1.62 -     1.82: 128
  Bond restraints: 20365
  Sorted by residual:
  bond pdb=" OAB NKN C 801 "
       pdb=" PAC NKN C 801 "
    ideal  model  delta    sigma   weight residual
    1.668  1.457  0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" OAB NKN B 801 "
       pdb=" PAC NKN B 801 "
    ideal  model  delta    sigma   weight residual
    1.668  1.459  0.209 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" OAA NKN B 801 "
       pdb=" PAC NKN B 801 "
    ideal  model  delta    sigma   weight residual
    1.667  1.458  0.209 2.00e-02 2.50e+03 1.09e+02
  bond pdb=" OAA NKN C 801 "
       pdb=" PAC NKN C 801 "
    ideal  model  delta    sigma   weight residual
    1.667  1.460  0.207 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" CAG NKN C 801 "
       pdb=" OAF NKN C 801 "
    ideal  model  delta    sigma   weight residual
    1.467  1.397  0.070 2.00e-02 2.50e+03 1.22e+01
  ... (remaining 20360 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.07: 36568
       10.07 -    20.14: 6
       20.14 -    30.22: 6
       30.22 -    40.29: 0
       40.29 -    50.36: 5
  Bond angle restraints: 36585
  Sorted by residual:
  angle pdb=" OAA NKN C 801 "
        pdb=" PAC NKN C 801 "
        pdb=" OAB NKN C 801 "
      ideal   model   delta    sigma   weight residual
      54.49  104.85  -50.36 3.00e+00 1.11e-01 2.82e+02
  angle pdb=" OAA NKN B 801 "
        pdb=" PAC NKN B 801 "
        pdb=" OAB NKN B 801 "
      ideal   model   delta    sigma   weight residual
      54.49  104.48  -49.99 3.00e+00 1.11e-01 2.78e+02
  angle pdb=" C23 8IJ A 801 "
        pdb=" C21 8IJ A 801 "
        pdb=" O20 8IJ A 801 "
      ideal   model   delta    sigma   weight residual
     112.40  160.53  -48.13 3.00e+00 1.11e-01 2.57e+02
  angle pdb=" O20 8IJ A 801 "
        pdb=" C21 8IJ A 801 "
        pdb=" O22 8IJ A 801 "
      ideal   model   delta    sigma   weight residual
     123.25   77.61   45.64 3.00e+00 1.11e-01 2.31e+02
  angle pdb=" C23 8IJ A 801 "
        pdb=" C21 8IJ A 801 "
        pdb=" O22 8IJ A 801 "
      ideal   model   delta    sigma   weight residual
     124.34   82.92   41.42 3.00e+00 1.11e-01 1.91e+02
  ... (remaining 36580 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.12: 9288
       31.12 -    62.23: 389
       62.23 -    93.35: 35
       93.35 -   124.47: 4
      124.47 -   155.59: 3
  Dihedral angle restraints: 9719
    sinusoidal: 5139
      harmonic: 4580
  Sorted by residual:
  dihedral pdb=" CD  ARG A 409 "
           pdb=" NE  ARG A 409 "
           pdb=" CZ  ARG A 409 "
           pdb=" NH1 ARG A 409 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -56.57   56.57     1      1.00e+01 1.00e-02 4.31e+01
  dihedral pdb=" CD  ARG B 409 "
           pdb=" NE  ARG B 409 "
           pdb=" CZ  ARG B 409 "
           pdb=" NH1 ARG B 409 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -48.08   48.08     1      1.00e+01 1.00e-02 3.19e+01
  dihedral pdb=" C49 8IJ D 801 "
           pdb=" C50 8IJ D 801 "
           pdb=" C51 8IJ D 801 "
           pdb=" C52 8IJ D 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.66  -32.75 -155.59     1      3.00e+01 1.11e-03 2.04e+01
  ... (remaining 9716 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.036: 1558
       1.036 -    2.072: 0
       2.072 -    3.108: 0
       3.108 -    4.144: 0
       4.144 -    5.180: 2
  Chirality restraints: 1560
  Sorted by residual:
  chirality pdb=" CAH NKN C 801 "
            pdb=" CAG NKN C 801 "
            pdb=" CAI NKN C 801 "
            pdb=" OAY NKN C 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.67    2.51   -5.18 2.00e-01 2.50e+01 6.71e+02
  chirality pdb=" C18 8IJ A 801 "
            pdb=" C17 8IJ A 801 "
            pdb=" C19 8IJ A 801 "
            pdb=" O40 8IJ A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.58    2.54   -5.12 2.00e-01 2.50e+01 6.55e+02
  chirality pdb=" CA  SER D 510 "
            pdb=" N   SER D 510 "
            pdb=" C   SER D 510 "
            pdb=" CB  SER D 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1557 not shown)

  Planarity restraints: 2839
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 474 "   -0.613 9.50e-02 1.11e+02   2.68e-01 7.25e+02
        pdb=" NE  ARG D 474 "   -0.137 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 474 "   -0.033 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 474 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 474 "    0.042 2.00e-02 2.50e+03
        pdb="HH11 ARG D 474 "    0.362 2.00e-02 2.50e+03
        pdb="HH12 ARG D 474 "   -0.335 2.00e-02 2.50e+03
        pdb="HH21 ARG D 474 "    0.059 2.00e-02 2.50e+03
        pdb="HH22 ARG D 474 "    0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 575 "   -0.217 9.50e-02 1.11e+02   1.74e-01 5.73e+02
        pdb=" NE  ARG B 575 "   -0.174 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 575 "   -0.052 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 575 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 575 "    0.034 2.00e-02 2.50e+03
        pdb="HH11 ARG B 575 "    0.325 2.00e-02 2.50e+03
        pdb="HH12 ARG B 575 "   -0.261 2.00e-02 2.50e+03
        pdb="HH21 ARG B 575 "    0.138 2.00e-02 2.50e+03
        pdb="HH22 ARG B 575 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 455 "    0.509 9.50e-02 1.11e+02   2.09e-01 3.69e+02
        pdb=" NE  ARG B 455 "    0.082 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 455 "    0.025 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 455 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 455 "   -0.031 2.00e-02 2.50e+03
        pdb="HH11 ARG B 455 "   -0.250 2.00e-02 2.50e+03
        pdb="HH12 ARG B 455 "    0.241 2.00e-02 2.50e+03
        pdb="HH21 ARG B 455 "   -0.019 2.00e-02 2.50e+03
        pdb="HH22 ARG B 455 "   -0.079 2.00e-02 2.50e+03
  ... (remaining 2836 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 1797
        2.23 -     2.82: 43382
        2.82 -     3.41: 54489
        3.41 -     4.01: 69831
        4.01 -     4.60: 107916
  Nonbonded interactions: 277415
  Sorted by model distance:
  nonbonded pdb="HD21 ASN B 408 "
            pdb=" OD2 ASP B 411 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" HZ3 LYS B 656 "
            pdb=" OH  TYR C 631 "
     model   vdw
     1.638 2.450
  nonbonded pdb=" OG  SER B 402 "
            pdb=" HG1 THR B 406 "
     model   vdw
     1.647 2.450
  nonbonded pdb=" OE1 GLN C 561 "
            pdb=" H   GLN C 561 "
     model   vdw
     1.647 2.450
  nonbonded pdb=" HH  TYR D 463 "
            pdb=" OH  TYR D 537 "
     model   vdw
     1.666 2.450
  ... (remaining 277410 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ 
ugh 683 or resid 688 through 712))
  selection = (chain 'B' and resid 392 through 712)
  selection = (chain 'C' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ 
ugh 683 or resid 688 through 712))
  selection = (chain 'D' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ 
ugh 683 or resid 688 through 712))
}

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:                  0.010
  Normalize map: mean=0, sd=1:             4.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.140
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     19.580
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
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      :  0.007   0.211  10309  Z= 0.378
  Angle     :  1.340  50.362  13911  Z= 0.626
  Chirality :  0.189   5.180   1560
  Planarity :  0.016   0.409   1673
  Dihedral  : 17.687 155.586   3831
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  2.56 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  1.43 (0.25), residues: 1179
  helix:  1.83 (0.17), residues: 890
  sheet:  None (None), residues: 0
  loop : -1.93 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 575 
 TYR   0.012   0.001   TYR B 627 
 PHE   0.021   0.001   PHE A 490 
 TRP   0.008   0.001   TRP B 697 
 HIS   0.002   0.001   HIS B 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00670 /  0.38 (10309)
  covalent geometry    : angle       1.34027 /  0.63 (13911)
  hydrogen bonds       : bond        0.11347 /  6.92 (  740)
  hydrogen bonds       : angle       5.05073 /  3.63 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 301
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  570 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7420 (tm-30)
REVERT: A  669 LEU cc_start: 0.8573 (mm) cc_final: 0.8264 (mm)
REVERT: D  439 PHE cc_start: 0.7782 (t80) cc_final: 0.7204 (t80)
REVERT: D  681 LEU cc_start: 0.8448 (mm) cc_final: 0.8220 (mm)
REVERT: B  579 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7045 (ptt180)
REVERT: B  631 TYR cc_start: 0.7656 (t80) cc_final: 0.7211 (t80)
  outliers start: 7
  outliers final: 3
  residues processed: 306
  average time/residue: 0.2299
  time to fit residues: 99.3224
Evaluate side-chains
  279 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 276
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  679 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 519 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.156132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.139199 restraints weight = 41685.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.143283 restraints weight = 17545.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.145892 restraints weight = 10055.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.147533 restraints weight = 6918.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.148587 restraints weight = 5336.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.0991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10309  Z= 0.198
  Angle     :  0.579   8.232  13911  Z= 0.316
  Chirality :  0.035   0.206   1560
  Planarity :  0.006   0.155   1673
  Dihedral  : 13.336 125.577   1513
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.34 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  1.76 (0.25), residues: 1179
  helix:  2.05 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -2.00 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 557 
 TYR   0.010   0.001   TYR A 511 
 PHE   0.012   0.001   PHE C 439 
 TRP   0.007   0.001   TRP B 697 
 HIS   0.002   0.001   HIS B 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00426 /  0.20 (10309)
  covalent geometry    : angle       0.57882 /  0.32 (13911)
  hydrogen bonds       : bond        0.05573 /  3.65 (  740)
  hydrogen bonds       : angle       4.32864 /  3.07 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 274
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  570 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7514 (tm-30)
REVERT: A  669 LEU cc_start: 0.8572 (mm) cc_final: 0.8269 (mm)
REVERT: A  707 ASP cc_start: 0.7552 (m-30) cc_final: 0.7217 (t0)
REVERT: D  439 PHE cc_start: 0.7787 (t80) cc_final: 0.7181 (t80)
REVERT: D  681 LEU cc_start: 0.8512 (mm) cc_final: 0.8311 (mm)
REVERT: B  523 MET cc_start: 0.7327 (tpt) cc_final: 0.7105 (tpt)
REVERT: B  579 ARG cc_start: 0.7586 (ptm160) cc_final: 0.7279 (ptm160)
REVERT: B  631 TYR cc_start: 0.7699 (t80) cc_final: 0.7432 (t80)
REVERT: C  471 ASP cc_start: 0.6332 (m-30) cc_final: 0.6114 (m-30)
REVERT: C  498 GLN cc_start: 0.6345 (mt0) cc_final: 0.6113 (mt0)
REVERT: C  652 ASN cc_start: 0.5316 (OUTLIER) cc_final: 0.4764 (m110)
  outliers start: 17
  outliers final: 14
  residues processed: 282
  average time/residue: 0.2283
  time to fit residues: 91.3191
Evaluate side-chains
  281 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 266
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain D residue  519 GLN
Chi-restraints excluded: chain D residue  630 LEU
Chi-restraints excluded: chain B residue  426 TRP
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  682 MET
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  520 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  672 ILE
Chi-restraints excluded: chain C residue  679 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 519 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.156971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.139987 restraints weight = 41705.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.144126 restraints weight = 17483.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.146738 restraints weight = 10017.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.148383 restraints weight = 6890.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.149470 restraints weight = 5313.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10309  Z= 0.158
  Angle     :  0.522   5.482  13911  Z= 0.289
  Chirality :  0.034   0.123   1560
  Planarity :  0.004   0.097   1673
  Dihedral  : 12.271 107.853   1513
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.90 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  2.07 (0.25), residues: 1179
  helix:  2.30 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.97 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 420 
 TYR   0.009   0.001   TYR A 555 
 PHE   0.011   0.001   PHE C 439 
 TRP   0.008   0.001   TRP B 697 
 HIS   0.001   0.000   HIS B 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.16 (10309)
  covalent geometry    : angle       0.52178 /  0.29 (13911)
  hydrogen bonds       : bond        0.05248 /  3.44 (  740)
  hydrogen bonds       : angle       4.16906 /  2.96 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 270
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  570 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7514 (tm-30)
REVERT: A  669 LEU cc_start: 0.8584 (mm) cc_final: 0.8261 (mm)
REVERT: A  707 ASP cc_start: 0.7600 (m-30) cc_final: 0.7308 (t0)
REVERT: D  439 PHE cc_start: 0.7775 (t80) cc_final: 0.7173 (t80)
REVERT: D  560 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6361 (pm20)
REVERT: B  579 ARG cc_start: 0.7662 (ptm160) cc_final: 0.7375 (ptm160)
REVERT: B  631 TYR cc_start: 0.7696 (t80) cc_final: 0.7422 (t80)
REVERT: B  677 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6684 (ttp)
REVERT: C  498 GLN cc_start: 0.6404 (mt0) cc_final: 0.6194 (mt0)
REVERT: C  652 ASN cc_start: 0.5275 (OUTLIER) cc_final: 0.4557 (m-40)
REVERT: C  677 MET cc_start: 0.7269 (tmm) cc_final: 0.7020 (tmm)
REVERT: C  709 GLU cc_start: 0.4988 (tm-30) cc_final: 0.4780 (tp30)
  outliers start: 18
  outliers final: 12
  residues processed: 279
  average time/residue: 0.2276
  time to fit residues: 90.0392
Evaluate side-chains
  275 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 260
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  560 GLN
Chi-restraints excluded: chain D residue  630 LEU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  677 MET
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  520 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  679 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 560 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.155111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.137883 restraints weight = 42031.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.141945 restraints weight = 17999.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.144504 restraints weight = 10503.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.146121 restraints weight = 7336.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.147187 restraints weight = 5726.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10309  Z= 0.216
  Angle     :  0.569   5.876  13911  Z= 0.316
  Chirality :  0.035   0.120   1560
  Planarity :  0.004   0.088   1673
  Dihedral  : 11.950  86.090   1513
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.64 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  1.57 (0.25), residues: 1179
  helix:  1.97 (0.17), residues: 911
  sheet:  None (None), residues: 0
  loop : -2.39 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 701 
 TYR   0.013   0.002   TYR A 555 
 PHE   0.015   0.001   PHE C 439 
 TRP   0.006   0.001   TRP B 697 
 HIS   0.002   0.001   HIS C 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.22 (10309)
  covalent geometry    : angle       0.56945 /  0.32 (13911)
  hydrogen bonds       : bond        0.05551 /  3.67 (  740)
  hydrogen bonds       : angle       4.32241 /  3.07 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 269
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  560 GLN cc_start: 0.7295 (tp-100) cc_final: 0.7031 (tp40)
REVERT: A  570 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7581 (tm-30)
REVERT: A  669 LEU cc_start: 0.8613 (mm) cc_final: 0.8202 (mm)
REVERT: A  707 ASP cc_start: 0.7604 (m-30) cc_final: 0.7267 (t0)
REVERT: D  439 PHE cc_start: 0.7855 (t80) cc_final: 0.7210 (t80)
REVERT: D  560 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6370 (pm20)
REVERT: B  579 ARG cc_start: 0.7738 (ptm160) cc_final: 0.7424 (ptm160)
REVERT: B  631 TYR cc_start: 0.7766 (t80) cc_final: 0.7449 (t80)
REVERT: B  677 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6565 (ttp)
REVERT: C  498 GLN cc_start: 0.6429 (mt0) cc_final: 0.6170 (mt0)
REVERT: C  677 MET cc_start: 0.7246 (tmm) cc_final: 0.7036 (tmm)
  outliers start: 23
  outliers final: 17
  residues processed: 281
  average time/residue: 0.2283
  time to fit residues: 90.9628
Evaluate side-chains
  279 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 260
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  538 VAL
Chi-restraints excluded: chain D residue  560 GLN
Chi-restraints excluded: chain D residue  630 LEU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  677 MET
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  520 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  660 ILE
Chi-restraints excluded: chain C residue  672 ILE
Chi-restraints excluded: chain C residue  679 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 116 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 410 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.151386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.133924 restraints weight = 41479.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.138039 restraints weight = 17492.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.140672 restraints weight = 10024.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.142363 restraints weight = 6901.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.143512 restraints weight = 5302.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10309  Z= 0.131
  Angle     :  0.497   5.309  13911  Z= 0.274
  Chirality :  0.033   0.126   1560
  Planarity :  0.003   0.061   1673
  Dihedral  : 11.164  84.281   1513
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.84 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  2.11 (0.26), residues: 1179
  helix:  2.38 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -2.27 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 534 
 TYR   0.012   0.001   TYR A 554 
 PHE   0.010   0.001   PHE B 659 
 TRP   0.008   0.001   TRP B 697 
 HIS   0.001   0.000   HIS B 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 (10309)
  covalent geometry    : angle       0.49702 /  0.27 (13911)
  hydrogen bonds       : bond        0.04887 /  3.24 (  740)
  hydrogen bonds       : angle       4.00991 /  2.84 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 274
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  707 ASP cc_start: 0.7559 (m-30) cc_final: 0.7241 (t0)
REVERT: D  439 PHE cc_start: 0.7739 (t80) cc_final: 0.7111 (t80)
REVERT: D  560 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6512 (pm20)
REVERT: B  455 ARG cc_start: 0.7537 (ptt90) cc_final: 0.7287 (ptt90)
REVERT: B  523 MET cc_start: 0.6955 (tpt) cc_final: 0.6745 (tpt)
REVERT: B  579 ARG cc_start: 0.7666 (ptm160) cc_final: 0.7371 (ptm160)
REVERT: B  631 TYR cc_start: 0.7718 (t80) cc_final: 0.7409 (t80)
REVERT: C  498 GLN cc_start: 0.6444 (mt0) cc_final: 0.6167 (mt0)
  outliers start: 21
  outliers final: 17
  residues processed: 286
  average time/residue: 0.2257
  time to fit residues: 91.5204
Evaluate side-chains
  279 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 261
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain D residue  479 ILE
Chi-restraints excluded: chain D residue  538 VAL
Chi-restraints excluded: chain D residue  560 GLN
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  677 MET
Chi-restraints excluded: chain B residue  710 LYS
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  660 ILE
Chi-restraints excluded: chain C residue  679 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 70 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 96 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.156473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.139460 restraints weight = 41409.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.143540 restraints weight = 17378.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.146129 restraints weight = 9997.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.147766 restraints weight = 6890.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.148850 restraints weight = 5327.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10309  Z= 0.156
  Angle     :  0.511   5.268  13911  Z= 0.281
  Chirality :  0.033   0.127   1560
  Planarity :  0.003   0.059   1673
  Dihedral  : 11.060  84.898   1513
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.29 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  2.08 (0.25), residues: 1179
  helix:  2.36 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -2.30 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 534 
 TYR   0.011   0.001   TYR D 453 
 PHE   0.015   0.001   PHE D 438 
 TRP   0.009   0.001   TRP A 697 
 HIS   0.001   0.000   HIS C 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.16 (10309)
  covalent geometry    : angle       0.51102 /  0.28 (13911)
  hydrogen bonds       : bond        0.04944 /  3.27 (  740)
  hydrogen bonds       : angle       4.04800 /  2.87 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 265
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  707 ASP cc_start: 0.7590 (m-30) cc_final: 0.7297 (t0)
REVERT: D  439 PHE cc_start: 0.7691 (t80) cc_final: 0.7091 (t80)
REVERT: D  560 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6403 (pm20)
REVERT: B  455 ARG cc_start: 0.7571 (ptt90) cc_final: 0.7317 (ptt90)
REVERT: B  572 MET cc_start: 0.7165 (mtt) cc_final: 0.6812 (mtp)
REVERT: B  579 ARG cc_start: 0.7674 (ptm160) cc_final: 0.7437 (ptm160)
REVERT: B  631 TYR cc_start: 0.7730 (t80) cc_final: 0.7410 (t80)
REVERT: C  498 GLN cc_start: 0.6376 (mt0) cc_final: 0.6121 (mt0)
  outliers start: 27
  outliers final: 21
  residues processed: 280
  average time/residue: 0.2302
  time to fit residues: 91.4928
Evaluate side-chains
  286 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 264
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain D residue  479 ILE
Chi-restraints excluded: chain D residue  538 VAL
Chi-restraints excluded: chain D residue  560 GLN
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  677 MET
Chi-restraints excluded: chain B residue  710 LYS
Chi-restraints excluded: chain C residue  410 HIS
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  520 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  660 ILE
Chi-restraints excluded: chain C residue  679 ILE
Chi-restraints excluded: chain C residue  681 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0570
   chunk 87 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 73 optimal weight:    0.3980
   overall best weight:    0.5698

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.151578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.133905 restraints weight = 41732.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.138053 restraints weight = 17614.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.140723 restraints weight = 10105.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.142427 restraints weight = 6962.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.143484 restraints weight = 5356.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10309  Z= 0.136
  Angle     :  0.495   5.256  13911  Z= 0.272
  Chirality :  0.033   0.133   1560
  Planarity :  0.003   0.050   1673
  Dihedral  : 10.840  85.021   1513
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.84 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  2.24 (0.26), residues: 1179
  helix:  2.47 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -2.21 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.010   0.001   TYR D 453 
 PHE   0.015   0.001   PHE D 438 
 TRP   0.010   0.001   TRP A 697 
 HIS   0.001   0.000   HIS B 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.14 (10309)
  covalent geometry    : angle       0.49455 /  0.27 (13911)
  hydrogen bonds       : bond        0.04754 /  3.15 (  740)
  hydrogen bonds       : angle       3.95808 /  2.80 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 266
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6522 (m-30)
REVERT: D  439 PHE cc_start: 0.7665 (t80) cc_final: 0.7048 (t80)
REVERT: D  531 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7183 (m-80)
REVERT: D  560 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6321 (pm20)
REVERT: B  455 ARG cc_start: 0.7554 (ptt90) cc_final: 0.7300 (ptt90)
REVERT: B  631 TYR cc_start: 0.7716 (t80) cc_final: 0.7398 (t80)
REVERT: B  658 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7801 (m)
REVERT: C  498 GLN cc_start: 0.6453 (mt0) cc_final: 0.6184 (mt0)
  outliers start: 27
  outliers final: 22
  residues processed: 281
  average time/residue: 0.2208
  time to fit residues: 87.9294
Evaluate side-chains
  286 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 260
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain D residue  479 ILE
Chi-restraints excluded: chain D residue  531 PHE
Chi-restraints excluded: chain D residue  538 VAL
Chi-restraints excluded: chain D residue  552 MET
Chi-restraints excluded: chain D residue  560 GLN
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  677 MET
Chi-restraints excluded: chain B residue  710 LYS
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  520 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  660 ILE
Chi-restraints excluded: chain C residue  679 ILE
Chi-restraints excluded: chain C residue  681 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.154800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.137397 restraints weight = 41630.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.141549 restraints weight = 17550.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.144200 restraints weight = 10063.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.145879 restraints weight = 6924.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.146963 restraints weight = 5339.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10309  Z= 0.153
  Angle     :  0.511   5.225  13911  Z= 0.280
  Chirality :  0.033   0.135   1560
  Planarity :  0.003   0.050   1673
  Dihedral  : 10.735  86.727   1513
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.93 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  2.17 (0.25), residues: 1179
  helix:  2.43 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -2.27 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 579 
 TYR   0.012   0.001   TYR C 671 
 PHE   0.011   0.001   PHE C 439 
 TRP   0.007   0.001   TRP A 697 
 HIS   0.001   0.000   HIS C 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 (10309)
  covalent geometry    : angle       0.51068 /  0.28 (13911)
  hydrogen bonds       : bond        0.04827 /  3.19 (  740)
  hydrogen bonds       : angle       3.98968 /  2.83 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 267
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  707 ASP cc_start: 0.7653 (m-30) cc_final: 0.7316 (t0)
REVERT: D  439 PHE cc_start: 0.7602 (t80) cc_final: 0.6965 (t80)
REVERT: D  531 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7219 (m-80)
REVERT: D  560 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6366 (pm20)
REVERT: B  455 ARG cc_start: 0.7548 (ptt90) cc_final: 0.7295 (ptt90)
REVERT: B  572 MET cc_start: 0.7020 (mtt) cc_final: 0.6774 (mtp)
REVERT: B  579 ARG cc_start: 0.7684 (ptm160) cc_final: 0.7183 (ptt180)
REVERT: B  631 TYR cc_start: 0.7688 (t80) cc_final: 0.7358 (t80)
REVERT: B  658 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7819 (m)
REVERT: C  498 GLN cc_start: 0.6411 (mt0) cc_final: 0.6171 (mt0)
  outliers start: 29
  outliers final: 23
  residues processed: 282
  average time/residue: 0.2255
  time to fit residues: 90.6439
Evaluate side-chains
  289 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 263
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  541 MET
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain D residue  479 ILE
Chi-restraints excluded: chain D residue  531 PHE
Chi-restraints excluded: chain D residue  538 VAL
Chi-restraints excluded: chain D residue  560 GLN
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  677 MET
Chi-restraints excluded: chain B residue  710 LYS
Chi-restraints excluded: chain C residue  410 HIS
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  520 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  660 ILE
Chi-restraints excluded: chain C residue  679 ILE
Chi-restraints excluded: chain C residue  681 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 111 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 114 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.9380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.150928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.133553 restraints weight = 41495.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.137614 restraints weight = 17830.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.140194 restraints weight = 10315.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.141851 restraints weight = 7147.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.142894 restraints weight = 5534.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10309  Z= 0.179
  Angle     :  0.535   5.550  13911  Z= 0.295
  Chirality :  0.034   0.142   1560
  Planarity :  0.003   0.053   1673
  Dihedral  : 10.735  88.904   1513
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.12 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  1.95 (0.25), residues: 1179
  helix:  2.27 (0.17), residues: 911
  sheet:  None (None), residues: 0
  loop : -2.38 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.015   0.001   TYR C 671 
 PHE   0.013   0.001   PHE C 439 
 TRP   0.006   0.001   TRP B 697 
 HIS   0.001   0.000   HIS C 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.18 (10309)
  covalent geometry    : angle       0.53512 /  0.30 (13911)
  hydrogen bonds       : bond        0.05046 /  3.33 (  740)
  hydrogen bonds       : angle       4.07481 /  2.89 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 270
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  707 ASP cc_start: 0.7639 (m-30) cc_final: 0.7299 (t0)
REVERT: D  439 PHE cc_start: 0.7711 (t80) cc_final: 0.7090 (t80)
REVERT: D  531 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7231 (m-80)
REVERT: D  560 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6319 (pm20)
REVERT: B  579 ARG cc_start: 0.7678 (ptm160) cc_final: 0.7019 (ptt180)
REVERT: B  631 TYR cc_start: 0.7738 (t80) cc_final: 0.7380 (t80)
REVERT: B  658 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7804 (m)
REVERT: C  498 GLN cc_start: 0.6413 (mt0) cc_final: 0.6156 (mt0)
  outliers start: 28
  outliers final: 23
  residues processed: 285
  average time/residue: 0.2233
  time to fit residues: 91.0278
Evaluate side-chains
  293 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 267
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  541 MET
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain D residue  479 ILE
Chi-restraints excluded: chain D residue  481 SER
Chi-restraints excluded: chain D residue  531 PHE
Chi-restraints excluded: chain D residue  538 VAL
Chi-restraints excluded: chain D residue  560 GLN
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  677 MET
Chi-restraints excluded: chain B residue  710 LYS
Chi-restraints excluded: chain C residue  410 HIS
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  520 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  660 ILE
Chi-restraints excluded: chain C residue  679 ILE
Chi-restraints excluded: chain C residue  681 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 117 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.151642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.134296 restraints weight = 41618.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.138376 restraints weight = 17908.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.140957 restraints weight = 10371.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.142631 restraints weight = 7200.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.143751 restraints weight = 5558.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10309  Z= 0.161
  Angle     :  0.523   6.128  13911  Z= 0.288
  Chirality :  0.033   0.143   1560
  Planarity :  0.003   0.050   1673
  Dihedral  : 10.632  89.993   1513
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.03 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  2.02 (0.25), residues: 1179
  helix:  2.31 (0.17), residues: 911
  sheet:  None (None), residues: 0
  loop : -2.33 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 534 
 TYR   0.012   0.001   TYR D 453 
 PHE   0.012   0.001   PHE C 439 
 TRP   0.006   0.001   TRP A 697 
 HIS   0.001   0.000   HIS B 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 (10309)
  covalent geometry    : angle       0.52328 /  0.29 (13911)
  hydrogen bonds       : bond        0.04947 /  3.27 (  740)
  hydrogen bonds       : angle       4.03601 /  2.86 ( 2181)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 269
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6589 (m-30)
REVERT: A  570 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7662 (tm-30)
REVERT: A  707 ASP cc_start: 0.7617 (m-30) cc_final: 0.7279 (t0)
REVERT: D  439 PHE cc_start: 0.7624 (t80) cc_final: 0.6993 (t80)
REVERT: D  531 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7222 (m-80)
REVERT: D  560 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6339 (pm20)
REVERT: B  579 ARG cc_start: 0.7704 (ptm160) cc_final: 0.7086 (ptt180)
REVERT: B  631 TYR cc_start: 0.7707 (t80) cc_final: 0.7350 (t80)
REVERT: B  658 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7802 (m)
REVERT: B  677 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6767 (ttp)
REVERT: C  498 GLN cc_start: 0.6414 (mt0) cc_final: 0.6183 (mt0)
  outliers start: 28
  outliers final: 22
  residues processed: 286
  average time/residue: 0.2280
  time to fit residues: 92.4818
Evaluate side-chains
  293 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 266
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  541 MET
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain D residue  479 ILE
Chi-restraints excluded: chain D residue  481 SER
Chi-restraints excluded: chain D residue  531 PHE
Chi-restraints excluded: chain D residue  538 VAL
Chi-restraints excluded: chain D residue  560 GLN
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  526 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  660 ILE
Chi-restraints excluded: chain B residue  667 VAL
Chi-restraints excluded: chain B residue  677 MET
Chi-restraints excluded: chain B residue  710 LYS
Chi-restraints excluded: chain C residue  410 HIS
Chi-restraints excluded: chain C residue  412 MET
Chi-restraints excluded: chain C residue  442 CYS
Chi-restraints excluded: chain C residue  457 VAL
Chi-restraints excluded: chain C residue  483 SER
Chi-restraints excluded: chain C residue  520 SER
Chi-restraints excluded: chain C residue  526 SER
Chi-restraints excluded: chain C residue  652 ASN
Chi-restraints excluded: chain C residue  660 ILE
Chi-restraints excluded: chain C residue  679 ILE
Chi-restraints excluded: chain C residue  681 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 63 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.151613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.134256 restraints weight = 41651.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.138304 restraints weight = 17951.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.140888 restraints weight = 10428.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.142546 restraints weight = 7253.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.143632 restraints weight = 5624.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10309  Z= 0.166
  Angle     :  0.529   6.362  13911  Z= 0.290
  Chirality :  0.034   0.150   1560
  Planarity :  0.003   0.051   1673
  Dihedral  : 10.568  89.178   1513
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.21 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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 are not related in a simple way.
  whole:  1.96 (0.25), residues: 1179
  helix:  2.27 (0.17), residues: 912
  sheet:  None (None), residues: 0
  loop : -2.36 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 534 
 TYR   0.013   0.001   TYR C 671 
 PHE   0.012   0.001   PHE C 439 
 TRP   0.005   0.001   TRP A 697 
 HIS   0.001   0.000   HIS C 410 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.17 (10309)
  covalent geometry    : angle       0.52880 /  0.29 (13911)
  hydrogen bonds       : bond        0.04978 /  3.29 (  740)
  hydrogen bonds       : angle       4.04978 /  2.87 ( 2181)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3601.15 seconds
wall clock time: 62 minutes 9.81 seconds (3729.81 seconds total)