Starting phenix.real_space_refine
on Fri Sep 11 16:30:23 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6ny1_8994/09_2026/6ny1_8994.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ny1_8994/09_2026/6ny1_8994.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6ny1_8994/09_2026/6ny1_8994.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6ny1_8994/09_2026/6ny1_8994.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ny1_8994/09_2026/6ny1_8994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ny1_8994/09_2026/6ny1_8994.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ny1_8994/09_2026/6ny1_8994.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ny1_8994/09_2026/6ny1_8994.cif"
  }
  resolution = 4.2
  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=   0.003 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 196 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     154      5.49       5
     S      20      5.16       5
     C    5724      2.51       5
     N    1805      2.21       5
     O    2208      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9911
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "Y"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 829
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "Y"
      Number of atoms: 4955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 667, 4955
          Classifications: {'peptide': 667}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 121}
          Link IDs: {'PTRANS': 22, 'TRANS': 644}
          Unresolved chain links: 1
          Chain breaks: 5
          Unresolved chain link angles: 4
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 359
          Unresolved non-hydrogen angles: 470
          Unresolved non-hydrogen dihedrals: 249
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'UNK:plan-1': 57, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 15, 'GLU:plan': 23, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 237
    Chain: "Y"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 887
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 153
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'UNK:plan-1': 64, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "D"
      Number of atoms: 346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 346
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "B"
      Number of atoms: 2300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 2300
          Classifications: {'RNAv2': 108}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 51, 'rna3p_pyr': 43}
          Link IDs: {'rna2p': 14, 'rna3p': 93}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 594
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
  Time building chain proxies: 2.40, per 1000 atoms: 0.24
  Number of scatterers: 9911
  At special positions: 0
  Unit cell: (99, 138.6, 120.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P     154     15.00
     O    2208      8.00
     N    1805      7.00
     C    5724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " UNK Y 104 " - " SER Y 103 "
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 260.0 milliseconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 5 sheets defined
      47.1% alpha, 7.5% beta
      54 base pairs and 86 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'Y' and resid 4 through 15
      removed outlier: 3.541A  pdb=" N   ASP Y  15 " --> pdb=" O   LYS Y  11 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 37 through 44
    Processing helix  chain 'Y' and resid 59 through 88
      removed outlier: 4.457A  pdb=" N   ASN Y  63 " --> pdb=" O   ASN Y  59 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN Y  64 " --> pdb=" O   ASN Y  60 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 90 through 98
    Processing helix  chain 'Y' and resid 194 through 198
    Processing helix  chain 'Y' and resid 222 through 260
      removed outlier: 3.755A  pdb=" N   ASP Y 245 " --> pdb=" O   SER Y 241 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 262 through 267
    Processing helix  chain 'Y' and resid 287 through 309
      removed outlier: 3.593A  pdb=" N   ASP Y 291 " --> pdb=" O   LYS Y 287 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 342 through 357
    Processing helix  chain 'Y' and resid 361 through 366
      removed outlier: 3.804A  pdb=" N   TRP Y 365 " --> pdb=" O   GLY Y 361 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER Y 366 " --> pdb=" O   ARG Y 362 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 361 through 366'
    Processing helix  chain 'Y' and resid 370 through 380
    Processing helix  chain 'Y' and resid 403 through 418
    Processing helix  chain 'Y' and resid 424 through 449
      removed outlier: 3.569A  pdb=" N   ARG Y 432 " --> pdb=" O   GLU Y 428 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS Y 436 " --> pdb=" O   ARG Y 432 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU Y 445 " --> pdb=" O   THR Y 441 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 456 through 473
      removed outlier: 3.746A  pdb=" N   VAL Y 460 " --> pdb=" O   GLN Y 456 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU Y 461 " --> pdb=" O   SER Y 457 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 474 through 476
      No H-bonds generated for 'chain 'Y' and resid 474 through 476'
    Processing helix  chain 'Y' and resid 483 through 501
      removed outlier: 3.840A  pdb=" N   CYS Y 487 " --> pdb=" O   GLU Y 483 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 502 through 504
      No H-bonds generated for 'chain 'Y' and resid 502 through 504'
    Processing helix  chain 'Y' and resid 602 through 610
    Processing helix  chain 'Y' and resid 711 through 728
      removed outlier: 3.541A  pdb=" N   ARG Y 727 " --> pdb=" O   GLU Y 723 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ARG Y 728 " --> pdb=" O   VAL Y 724 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 737 through 761
      removed outlier: 4.173A  pdb=" N   ARG Y 741 " --> pdb=" O   ALA Y 737 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 790 through 802
      removed outlier: 3.769A  pdb=" N   TYR Y 802 " --> pdb=" O   ALA Y 798 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 886 through 892
    Processing helix  chain 'Y' and resid 897 through 903
    Processing helix  chain 'Y' and resid 906 through 914
      removed outlier: 4.825A  pdb=" N   UNK Y 910 " --> pdb=" O   UNK Y 906 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 935 through 938
    Processing helix  chain 'Y' and resid 939 through 951
      removed outlier: 3.764A  pdb=" N   LEU Y 947 " --> pdb=" O   ALA Y 943 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN Y 950 " --> pdb=" O   TRP Y 946 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 965 through 978
    Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 19
    Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 6.921A  pdb=" N   THR Y 651 " --> pdb=" O   ALA Y 625 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29
      removed outlier: 6.921A  pdb=" N   THR Y 651 " --> pdb=" O   ALA Y 625 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Y' and resid 530 through 532
      removed outlier: 3.554A  pdb=" N   LEU Y 547 " --> pdb=" O   LEU Y 531 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 680 through 682
      removed outlier: 3.840A  pdb=" N   ALA Y 682 " --> pdb=" O   GLY Y 670 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   ILE Y 669 " --> pdb=" O   VAL Y 767 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    807 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      134 hydrogen bonds
      252 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      86 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1448
        1.32 -     1.44: 3542
        1.44 -     1.57: 5087
        1.57 -     1.69: 303
        1.69 -     1.81: 32
  Bond restraints: 10412
  Sorted by residual:
  bond pdb=" C3'  DA D   5 "
       pdb=" O3'  DA D   5 "
    ideal  model  delta    sigma   weight residual
    1.435  1.382  0.053 1.30e-02 5.92e+03 1.69e+01
  bond pdb=" C3'  DT D   8 "
       pdb=" C2'  DT D   8 "
    ideal  model  delta    sigma   weight residual
    1.516  1.548 -0.032 8.00e-03 1.56e+04 1.56e+01
  bond pdb=" C   ASP Y 685 "
       pdb=" N   PRO Y 686 "
    ideal  model  delta    sigma   weight residual
    1.330  1.377 -0.047 1.25e-02 6.40e+03 1.39e+01
  bond pdb=" C3'  DG C  19 "
       pdb=" O3'  DG C  19 "
    ideal  model  delta    sigma   weight residual
    1.435  1.387  0.048 1.30e-02 5.92e+03 1.39e+01
  bond pdb=" C3'  DA C  24 "
       pdb=" C2'  DA C  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.37e+01
  ... (remaining 10407 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.55: 14506
        3.55 -     7.10: 272
        7.10 -    10.65: 22
       10.65 -    14.20: 4
       14.20 -    17.75: 1
  Bond angle restraints: 14805
  Sorted by residual:
  angle pdb=" N   PHE Y 736 "
        pdb=" CA  PHE Y 736 "
        pdb=" C   PHE Y 736 "
      ideal   model   delta    sigma   weight residual
     110.91  124.49  -13.58 1.17e+00 7.31e-01 1.35e+02
  angle pdb=" C   LYS Y 735 "
        pdb=" N   PHE Y 736 "
        pdb=" CA  PHE Y 736 "
      ideal   model   delta    sigma   weight residual
     122.93  132.33   -9.40 1.51e+00 4.39e-01 3.88e+01
  angle pdb=" C3'   C B 111 "
        pdb=" O3'   C B 111 "
        pdb=" P     A B 112 "
      ideal   model   delta    sigma   weight residual
     119.70  126.88   -7.18 1.20e+00 6.94e-01 3.58e+01
  angle pdb=" O4'  DG D   2 "
        pdb=" C4'  DG D   2 "
        pdb=" C3'  DG D   2 "
      ideal   model   delta    sigma   weight residual
     106.00  102.42    3.58 6.00e-01 2.78e+00 3.56e+01
  angle pdb=" C   PHE Y 609 "
        pdb=" N   ILE Y 610 "
        pdb=" CA  ILE Y 610 "
      ideal   model   delta    sigma   weight residual
     123.16  117.10    6.06 1.06e+00 8.90e-01 3.26e+01
  ... (remaining 14800 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.46: 5348
       35.46 -    70.92: 484
       70.92 -   106.39: 25
      106.39 -   141.85: 2
      141.85 -   177.31: 6
  Dihedral angle restraints: 5865
    sinusoidal: 3242
      harmonic: 2623
  Sorted by residual:
  dihedral pdb=" C4'   U B  16 "
           pdb=" C3'   U B  16 "
           pdb=" C2'   U B  16 "
           pdb=" C1'   U B  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.86   75.20     1      3.10e+00 1.04e-01 7.44e+02
  dihedral pdb=" C4'   A B 114 "
           pdb=" C3'   A B 114 "
           pdb=" C2'   A B 114 "
           pdb=" C1'   A B 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.11   73.45     1      3.10e+00 1.04e-01 7.14e+02
  dihedral pdb=" CA  LYS Y 735 "
           pdb=" C   LYS Y 735 "
           pdb=" N   PHE Y 736 "
           pdb=" CA  PHE Y 736 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -47.13 -132.87     0      5.00e+00 4.00e-02 7.06e+02
  ... (remaining 5862 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1328
       0.072 -    0.144: 255
       0.144 -    0.217: 101
       0.217 -    0.289: 63
       0.289 -    0.361: 15
  Chirality restraints: 1762
  Sorted by residual:
  chirality pdb=" C3'   G B  30 "
            pdb=" C4'   G B  30 "
            pdb=" O3'   G B  30 "
            pdb=" C2'   G B  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.14   -0.36 2.00e-01 2.50e+01 3.26e+00
  chirality pdb=" C2'   C B 111 "
            pdb=" C3'   C B 111 "
            pdb=" O2'   C B 111 "
            pdb=" C1'   C B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.43   -0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" P     C B  61 "
            pdb=" OP1   C B  61 "
            pdb=" OP2   C B  61 "
            pdb=" O5'   C B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.52   -0.34 2.00e-01 2.50e+01 2.93e+00
  ... (remaining 1759 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 105 "    0.038 2.00e-02 2.50e+03   1.95e-02 8.53e+00
        pdb=" N1    C B 105 "   -0.028 2.00e-02 2.50e+03
        pdb=" C2    C B 105 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    C B 105 "   -0.018 2.00e-02 2.50e+03
        pdb=" N3    C B 105 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    C B 105 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C B 105 "    0.019 2.00e-02 2.50e+03
        pdb=" C5    C B 105 "   -0.020 2.00e-02 2.50e+03
        pdb=" C6    C B 105 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  52 "   -0.028 2.00e-02 2.50e+03   1.67e-02 8.39e+00
        pdb=" N9    G B  52 "    0.012 2.00e-02 2.50e+03
        pdb=" C8    G B  52 "    0.012 2.00e-02 2.50e+03
        pdb=" N7    G B  52 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    G B  52 "    0.010 2.00e-02 2.50e+03
        pdb=" C6    G B  52 "    0.020 2.00e-02 2.50e+03
        pdb=" O6    G B  52 "   -0.027 2.00e-02 2.50e+03
        pdb=" N1    G B  52 "   -0.022 2.00e-02 2.50e+03
        pdb=" C2    G B  52 "    0.022 2.00e-02 2.50e+03
        pdb=" N2    G B  52 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    G B  52 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G B  52 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY Y  25 "   -0.047 5.00e-02 4.00e+02   7.11e-02 8.08e+00
        pdb=" N   PRO Y  26 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO Y  26 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO Y  26 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 381
        2.66 -     3.22: 8575
        3.22 -     3.78: 17833
        3.78 -     4.34: 20284
        4.34 -     4.90: 29980
  Nonbonded interactions: 77053
  Sorted by model distance:
  nonbonded pdb=" O2'   C B  40 "
            pdb=" OP1   U B  41 "
     model   vdw
     2.099 3.040
  nonbonded pdb=" OD1 ASP Y 513 "
            pdb=" OG  SER Y 515 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR Y  29 "
            pdb=" O2    U B 103 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ALA Y 816 "
            pdb=" OG1 THR Y 819 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OH  TYR Y 382 "
            pdb=" O   SER Y 470 "
     model   vdw
     2.300 3.040
  ... (remaining 77048 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.010
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
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      :  0.008   0.053  10413  Z= 0.464
  Angle     :  1.211  17.747  14808  Z= 0.674
  Chirality :  0.086   0.361   1762
  Planarity :  0.008   0.071   1334
  Dihedral  : 22.613 177.312   4158
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 18.62 %
    Favored  : 80.99 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 12.71 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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: -4.83 (0.24), residues: 768
  helix: -2.46 (0.21), residues: 326
  sheet: -3.32 (0.56), residues: 73
  loop : -3.95 (0.27), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Y 753 
 TYR   0.020   0.003   TYR Y 418 
 PHE   0.033   0.003   PHE Y 609 
 TRP   0.025   0.003   TRP Y 534 
 HIS   0.009   0.002   HIS Y 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00752 /  0.46 (10412)
  covalent geometry    : angle       1.21060 /  0.67 (14805)
  hydrogen bonds       : bond        0.14230 /  9.22 (  404)
  hydrogen bonds       : angle       6.92977 /  4.90 ( 1059)
  link_TRANS           : bond        0.00388 /  0.20 (    1)
  link_TRANS           : angle       1.14797 /  0.65 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y    8 ILE cc_start: 0.9688 (mm) cc_final: 0.9352 (tt)
REVERT: Y   67 MET cc_start: 0.8116 (ttp) cc_final: 0.7738 (tpp)
REVERT: Y   75 MET cc_start: 0.8495 (mtm) cc_final: 0.8245 (mtp)
REVERT: Y  490 GLN cc_start: 0.9402 (tt0) cc_final: 0.9026 (tp-100)
REVERT: Y  747 MET cc_start: 0.9234 (tmm) cc_final: 0.8880 (tmm)
  outliers start: 2
  outliers final: 1
  residues processed: 94
  average time/residue: 0.1175
  time to fit residues: 15.2296
Evaluate side-chains
  63 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.098338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.073440 restraints weight = 32246.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.075906 restraints weight = 16027.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.077528 restraints weight = 10198.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.078557 restraints weight = 7691.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.079226 restraints weight = 6470.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10413  Z= 0.220
  Angle     :  1.234  28.012  14808  Z= 0.542
  Chirality :  0.119   3.204   1762
  Planarity :  0.006   0.070   1334
  Dihedral  : 22.986 178.758   2747
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 17.58 %
    Favored  : 82.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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: -3.74 (0.27), residues: 768
  helix: -1.01 (0.26), residues: 339
  sheet: -3.50 (0.52), residues: 78
  loop : -3.82 (0.29), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Y 749 
 TYR   0.015   0.002   TYR Y 536 
 PHE   0.039   0.002   PHE Y 736 
 TRP   0.026   0.002   TRP Y 534 
 HIS   0.008   0.002   HIS Y 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00430 /  0.22 (10412)
  covalent geometry    : angle       1.23403 /  0.54 (14805)
  hydrogen bonds       : bond        0.06784 /  4.55 (  404)
  hydrogen bonds       : angle       5.37753 /  3.75 ( 1059)
  link_TRANS           : bond        0.00159 /  0.08 (    1)
  link_TRANS           : angle       0.64854 /  0.35 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8245 (ttp) cc_final: 0.7830 (tpp)
REVERT: Y   75 MET cc_start: 0.8723 (mtm) cc_final: 0.8378 (mtp)
REVERT: Y  490 GLN cc_start: 0.9395 (tt0) cc_final: 0.9032 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7673 (m-80) cc_final: 0.7122 (m-80)
REVERT: Y  574 LEU cc_start: 0.9136 (tp) cc_final: 0.8836 (tp)
REVERT: Y  747 MET cc_start: 0.9238 (tmm) cc_final: 0.8881 (tmm)
REVERT: Y  977 ARG cc_start: 0.8832 (mmt-90) cc_final: 0.8531 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1034
  time to fit residues: 13.8481
Evaluate side-chains
  64 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:   30.0000
   chunk 16 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 44 optimal weight:    0.7980
   chunk 73 optimal weight:    0.1980
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.099458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.074879 restraints weight = 31855.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.077453 restraints weight = 15623.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.079157 restraints weight = 9751.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.080243 restraints weight = 7202.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.080918 restraints weight = 5987.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10413  Z= 0.181
  Angle     :  1.052  24.894  14808  Z= 0.473
  Chirality :  0.076   0.945   1762
  Planarity :  0.005   0.062   1334
  Dihedral  : 22.775 177.144   2747
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 16.80 %
    Favored  : 82.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -3.07 (0.29), residues: 768
  helix: -0.26 (0.27), residues: 331
  sheet: -3.22 (0.54), residues: 78
  loop : -3.61 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG Y 944 
 TYR   0.015   0.001   TYR Y 575 
 PHE   0.029   0.002   PHE Y 736 
 TRP   0.017   0.001   TRP Y 534 
 HIS   0.009   0.002   HIS Y 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.18 (10412)
  covalent geometry    : angle       1.05214 /  0.47 (14805)
  hydrogen bonds       : bond        0.06671 /  4.40 (  404)
  hydrogen bonds       : angle       5.05915 /  3.53 ( 1059)
  link_TRANS           : bond        0.00236 /  0.12 (    1)
  link_TRANS           : angle       0.17827 /  0.10 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8823 (mtm) cc_final: 0.8468 (mtp)
REVERT: Y  462 THR cc_start: 0.9444 (p) cc_final: 0.9151 (p)
REVERT: Y  490 GLN cc_start: 0.9409 (tt0) cc_final: 0.9058 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7530 (m-80) cc_final: 0.6979 (m-80)
REVERT: Y  747 MET cc_start: 0.9210 (tmm) cc_final: 0.8855 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0907
  time to fit residues: 12.6321
Evaluate side-chains
  63 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0370
   chunk 88 optimal weight:   30.0000
   chunk 83 optimal weight:   20.0000
   overall best weight:    2.5664

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.098613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.073866 restraints weight = 32286.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.076369 restraints weight = 15915.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.078043 restraints weight = 10094.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.079066 restraints weight = 7537.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.079747 restraints weight = 6331.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10413  Z= 0.197
  Angle     :  1.009  27.058  14808  Z= 0.456
  Chirality :  0.069   0.777   1762
  Planarity :  0.005   0.061   1334
  Dihedral  : 22.740 174.328   2747
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 18.10 %
    Favored  : 81.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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: -2.91 (0.29), residues: 768
  helix:  0.02 (0.28), residues: 333
  sheet: -3.35 (0.53), residues: 81
  loop : -3.65 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 944 
 TYR   0.013   0.001   TYR Y 196 
 PHE   0.019   0.002   PHE Y 609 
 TRP   0.019   0.002   TRP Y 343 
 HIS   0.016   0.003   HIS Y 206 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.20 (10412)
  covalent geometry    : angle       1.00874 /  0.46 (14805)
  hydrogen bonds       : bond        0.06332 /  4.15 (  404)
  hydrogen bonds       : angle       4.95206 /  3.45 ( 1059)
  link_TRANS           : bond        0.00195 /  0.10 (    1)
  link_TRANS           : angle       0.47146 /  0.27 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8823 (mtm) cc_final: 0.8509 (mtp)
REVERT: Y  490 GLN cc_start: 0.9404 (tt0) cc_final: 0.9066 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7614 (m-80) cc_final: 0.7062 (m-80)
REVERT: Y  747 MET cc_start: 0.9192 (tmm) cc_final: 0.8782 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.0876
  time to fit residues: 12.0091
Evaluate side-chains
  61 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:   20.0000
   chunk 78 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3757 r_free = 0.3757 target = 0.099760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.075249 restraints weight = 31955.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.077758 restraints weight = 15959.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.079421 restraints weight = 10144.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.080506 restraints weight = 7590.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.081054 restraints weight = 6340.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10413  Z= 0.168
  Angle     :  0.923  11.557  14808  Z= 0.424
  Chirality :  0.065   0.672   1762
  Planarity :  0.004   0.056   1334
  Dihedral  : 22.633 175.519   2747
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.67 %
    Favored  : 83.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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: -2.72 (0.29), residues: 768
  helix:  0.27 (0.28), residues: 332
  sheet: -3.20 (0.55), residues: 78
  loop : -3.66 (0.29), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 299 
 TYR   0.014   0.001   TYR Y 196 
 PHE   0.017   0.002   PHE Y 609 
 TRP   0.016   0.001   TRP Y 534 
 HIS   0.008   0.002   HIS Y 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.17 (10412)
  covalent geometry    : angle       0.92270 /  0.42 (14805)
  hydrogen bonds       : bond        0.06024 /  3.94 (  404)
  hydrogen bonds       : angle       4.76030 /  3.32 ( 1059)
  link_TRANS           : bond        0.00198 /  0.10 (    1)
  link_TRANS           : angle       0.28046 /  0.16 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   67 MET cc_start: 0.8127 (ttp) cc_final: 0.7895 (ttm)
REVERT: Y   75 MET cc_start: 0.8766 (mtm) cc_final: 0.8443 (mtp)
REVERT: Y   95 MET cc_start: 0.8042 (mtm) cc_final: 0.7831 (mtt)
REVERT: Y  462 THR cc_start: 0.9437 (p) cc_final: 0.9221 (p)
REVERT: Y  490 GLN cc_start: 0.9360 (tt0) cc_final: 0.9056 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7540 (m-80) cc_final: 0.7214 (m-80)
REVERT: Y  747 MET cc_start: 0.8503 (tmm) cc_final: 0.7715 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0740
  time to fit residues: 10.1061
Evaluate side-chains
  60 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 50 optimal weight:    0.0570
   chunk 87 optimal weight:   50.0000
   chunk 61 optimal weight:    5.9990
   chunk 84 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 88 optimal weight:   30.0000
   chunk 28 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   overall best weight:    4.4106

-------------------------------------------------------------------------------
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 = 0.3702 r_free = 0.3702 target = 0.096542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.071828 restraints weight = 32795.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.074213 restraints weight = 16422.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.075779 restraints weight = 10556.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.076723 restraints weight = 7981.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.077389 restraints weight = 6771.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  10413  Z= 0.275
  Angle     :  1.019  11.234  14808  Z= 0.468
  Chirality :  0.065   0.634   1762
  Planarity :  0.005   0.058   1334
  Dihedral  : 22.649 173.160   2747
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 17.73
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 18.23 %
    Favored  : 81.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.92 (0.29), residues: 768
  helix:  0.13 (0.28), residues: 336
  sheet: -3.38 (0.54), residues: 81
  loop : -3.82 (0.29), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Y 944 
 TYR   0.016   0.002   TYR Y 536 
 PHE   0.020   0.002   PHE Y 544 
 TRP   0.016   0.002   TRP Y 795 
 HIS   0.006   0.002   HIS Y 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00556 /  0.28 (10412)
  covalent geometry    : angle       1.01857 /  0.47 (14805)
  hydrogen bonds       : bond        0.07147 /  4.60 (  404)
  hydrogen bonds       : angle       4.98307 /  3.52 ( 1059)
  link_TRANS           : bond        0.00268 /  0.14 (    1)
  link_TRANS           : angle       0.69431 /  0.40 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8818 (mtm) cc_final: 0.8531 (mtp)
REVERT: Y  490 GLN cc_start: 0.9397 (tt0) cc_final: 0.9074 (tp-100)
REVERT: Y  548 MET cc_start: 0.8119 (ttt) cc_final: 0.7873 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0899
  time to fit residues: 11.7267
Evaluate side-chains
  56 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 0 optimal weight:    9.9990
   chunk 87 optimal weight:   50.0000
   chunk 69 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 10 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.095189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.070397 restraints weight = 32800.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.072727 restraints weight = 16630.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.074257 restraints weight = 10782.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.075227 restraints weight = 8207.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.075724 restraints weight = 6957.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  10413  Z= 0.309
  Angle     :  1.058  11.027  14808  Z= 0.487
  Chirality :  0.067   0.625   1762
  Planarity :  0.005   0.059   1334
  Dihedral  : 22.607 172.501   2747
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 19.40 %
    Favored  : 80.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.99 (0.29), residues: 768
  helix:  0.17 (0.28), residues: 330
  sheet: -3.49 (0.53), residues: 81
  loop : -3.88 (0.28), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Y 432 
 TYR   0.016   0.002   TYR Y 536 
 PHE   0.021   0.003   PHE Y 544 
 TRP   0.021   0.002   TRP Y 464 
 HIS   0.007   0.002   HIS Y 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00630 /  0.31 (10412)
  covalent geometry    : angle       1.05783 /  0.49 (14805)
  hydrogen bonds       : bond        0.07377 /  4.83 (  404)
  hydrogen bonds       : angle       5.10014 /  3.60 ( 1059)
  link_TRANS           : bond        0.00346 /  0.18 (    1)
  link_TRANS           : angle       0.57822 /  0.33 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8797 (mtm) cc_final: 0.8473 (mtp)
REVERT: Y   95 MET cc_start: 0.8280 (mtm) cc_final: 0.8054 (mtt)
REVERT: Y  490 GLN cc_start: 0.9404 (tt0) cc_final: 0.9042 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7529 (m-80) cc_final: 0.7223 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0920
  time to fit residues: 10.8995
Evaluate side-chains
  55 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   chunk 14 optimal weight:   20.0000
   chunk 59 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:   20.0000
   chunk 27 optimal weight:    6.9990
   chunk 42 optimal weight:    0.4980
   chunk 57 optimal weight:    2.9990
   overall best weight:    2.2988

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.098149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.073546 restraints weight = 31809.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.076010 restraints weight = 15824.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.077650 restraints weight = 10065.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.078681 restraints weight = 7543.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.079205 restraints weight = 6327.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10413  Z= 0.189
  Angle     :  0.943   9.856  14808  Z= 0.436
  Chirality :  0.063   0.607   1762
  Planarity :  0.005   0.055   1334
  Dihedral  : 22.462 173.518   2747
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 17.45 %
    Favored  : 82.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.84 (0.29), residues: 768
  helix:  0.22 (0.28), residues: 333
  sheet: -3.49 (0.52), residues: 81
  loop : -3.72 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y 299 
 TYR   0.023   0.002   TYR Y 293 
 PHE   0.021   0.002   PHE Y 609 
 TRP   0.019   0.002   TRP Y 464 
 HIS   0.010   0.002   HIS Y 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.19 (10412)
  covalent geometry    : angle       0.94281 /  0.44 (14805)
  hydrogen bonds       : bond        0.06297 /  4.14 (  404)
  hydrogen bonds       : angle       4.84489 /  3.43 ( 1059)
  link_TRANS           : bond        0.00174 /  0.09 (    1)
  link_TRANS           : angle       0.52129 /  0.29 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: Y   75 MET cc_start: 0.8817 (mtm) cc_final: 0.8512 (mtp)
REVERT: Y   95 MET cc_start: 0.8167 (mtm) cc_final: 0.7963 (mtt)
REVERT: Y  490 GLN cc_start: 0.9414 (tt0) cc_final: 0.9040 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7484 (m-80) cc_final: 0.7137 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.0820
  time to fit residues: 11.3917
Evaluate side-chains
  59 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 81 optimal weight:    8.9990
   chunk 63 optimal weight:    0.4980
   chunk 13 optimal weight:   30.0000
   chunk 9 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 88 optimal weight:   30.0000
   chunk 64 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    3.0986

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.097244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.072576 restraints weight = 32465.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.074975 restraints weight = 16280.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.076576 restraints weight = 10471.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.077592 restraints weight = 7922.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.078240 restraints weight = 6673.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10413  Z= 0.219
  Angle     :  0.955   9.820  14808  Z= 0.441
  Chirality :  0.063   0.558   1762
  Planarity :  0.005   0.053   1334
  Dihedral  : 22.450 173.784   2747
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 18.36 %
    Favored  : 81.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.76 (0.29), residues: 768
  helix:  0.27 (0.28), residues: 331
  sheet: -3.51 (0.52), residues: 81
  loop : -3.63 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Y 749 
 TYR   0.016   0.002   TYR Y 382 
 PHE   0.021   0.002   PHE Y 609 
 TRP   0.017   0.002   TRP Y 795 
 HIS   0.008   0.002   HIS Y 206 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.22 (10412)
  covalent geometry    : angle       0.95534 /  0.44 (14805)
  hydrogen bonds       : bond        0.06616 /  4.35 (  404)
  hydrogen bonds       : angle       4.85312 /  3.45 ( 1059)
  link_TRANS           : bond        0.00259 /  0.14 (    1)
  link_TRANS           : angle       0.42964 /  0.25 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: Y   27 MET cc_start: 0.6933 (mmt) cc_final: 0.6660 (mmt)
REVERT: Y   75 MET cc_start: 0.8808 (mtm) cc_final: 0.8496 (mtp)
REVERT: Y  462 THR cc_start: 0.9448 (p) cc_final: 0.9242 (p)
REVERT: Y  490 GLN cc_start: 0.9401 (tt0) cc_final: 0.9036 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7516 (m-80) cc_final: 0.7167 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0862
  time to fit residues: 11.6153
Evaluate side-chains
  59 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 88 optimal weight:   30.0000
   chunk 65 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 57 optimal weight:    0.3980
   chunk 35 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.4382

-------------------------------------------------------------------------------
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 = 0.3762 r_free = 0.3762 target = 0.100108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.075479 restraints weight = 31634.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.078007 restraints weight = 15854.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.079659 restraints weight = 10107.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.080732 restraints weight = 7632.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.081288 restraints weight = 6415.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10413  Z= 0.157
  Angle     :  0.898   9.462  14808  Z= 0.415
  Chirality :  0.061   0.534   1762
  Planarity :  0.004   0.049   1334
  Dihedral  : 22.335 174.674   2747
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.80 %
    Favored  : 83.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.62 (0.29), residues: 768
  helix:  0.38 (0.28), residues: 331
  sheet: -3.42 (0.52), residues: 81
  loop : -3.54 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Y 753 
 TYR   0.012   0.001   TYR Y 196 
 PHE   0.020   0.002   PHE Y 609 
 TRP   0.020   0.002   TRP Y 344 
 HIS   0.005   0.001   HIS Y 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.16 (10412)
  covalent geometry    : angle       0.89810 /  0.41 (14805)
  hydrogen bonds       : bond        0.05960 /  3.97 (  404)
  hydrogen bonds       : angle       4.68078 /  3.33 ( 1059)
  link_TRANS           : bond        0.00140 /  0.07 (    1)
  link_TRANS           : angle       0.46996 /  0.26 (    3)

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.471 
Fit side-chains
REVERT: Y   27 MET cc_start: 0.6578 (mmt) cc_final: 0.6339 (mmt)
REVERT: Y   75 MET cc_start: 0.8798 (mtm) cc_final: 0.8483 (mtp)
REVERT: Y  462 THR cc_start: 0.9379 (p) cc_final: 0.9061 (p)
REVERT: Y  490 GLN cc_start: 0.9405 (tt0) cc_final: 0.9046 (tp-100)
REVERT: Y  550 TYR cc_start: 0.7545 (m-80) cc_final: 0.7335 (m-80)
REVERT: Y  747 MET cc_start: 0.8535 (tmm) cc_final: 0.7774 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0772
  time to fit residues: 10.6192
Evaluate side-chains
  57 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0030
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 83 optimal weight:   20.0000
   chunk 70 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    2.5998

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.098706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.074008 restraints weight = 32040.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.076471 restraints weight = 16168.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.078091 restraints weight = 10368.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.079133 restraints weight = 7834.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.079816 restraints weight = 6580.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10413  Z= 0.196
  Angle     :  0.914   9.470  14808  Z= 0.422
  Chirality :  0.061   0.488   1762
  Planarity :  0.004   0.049   1334
  Dihedral  : 22.339 174.459   2747
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 17.84 %
    Favored  : 82.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.53 (0.30), residues: 768
  helix:  0.47 (0.28), residues: 333
  sheet: -3.32 (0.52), residues: 81
  loop : -3.55 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y 753 
 TYR   0.014   0.002   TYR Y 382 
 PHE   0.020   0.002   PHE Y 609 
 TRP   0.017   0.002   TRP Y 795 
 HIS   0.005   0.001   HIS Y 443 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.20 (10412)
  covalent geometry    : angle       0.91428 /  0.42 (14805)
  hydrogen bonds       : bond        0.06249 /  4.16 (  404)
  hydrogen bonds       : angle       4.69284 /  3.36 ( 1059)
  link_TRANS           : bond        0.00214 /  0.11 (    1)
  link_TRANS           : angle       0.42848 /  0.25 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1856.38 seconds
wall clock time: 32 minutes 49.83 seconds (1969.83 seconds total)