Starting phenix.real_space_refine
on Thu Mar  5 00:11:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z4c_14493/03_2026/7z4c_14493.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z4c_14493/03_2026/7z4c_14493.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z4c_14493/03_2026/7z4c_14493.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z4c_14493/03_2026/7z4c_14493.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z4c_14493/03_2026/7z4c_14493.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z4c_14493/03_2026/7z4c_14493.map"
  }
  resolution = 3.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.021
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 3714 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     145      5.49       5
     S      23      5.16       5
     C    8486      2.51       5
     N    2483      2.21       5
     O    3043      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14180
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 589
          Classifications: {'DNA': 29}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 28}
    Chain: "D"
      Number of atoms: 592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 592
          Classifications: {'DNA': 29}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 28}
    Chain: "A"
      Number of atoms: 1910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 1910
          Classifications: {'DNA': 1, 'RNA': 89}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 13, 'rna3p': 76}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  A%5*END:plan': 1, '  A%5*END:plan2': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 11089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1357, 11089
          Classifications: {'peptide': 1357}
          Link IDs: {'PTRANS': 35, 'TRANS': 1321}
          Chain breaks: 1
  Time building chain proxies: 3.14, per 1000 atoms: 0.22
  Number of scatterers: 14180
  At special positions: 0
  Unit cell: (92.3, 124.15, 124.8, 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      23     16.00
     P     145     15.00
     O    3043      8.00
     N    2483      7.00
     C    8486      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 693.5 milliseconds
  

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 10 sheets defined
      54.4% alpha, 8.1% beta
      51 base pairs and 93 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'B' and resid 59 through 86
    Processing helix  chain 'B' and resid 86 through 94
    Processing helix  chain 'B' and resid 96 through 103
    Processing helix  chain 'B' and resid 107 through 111
    Processing helix  chain 'B' and resid 121 through 132
    Processing helix  chain 'B' and resid 134 through 145
    Processing helix  chain 'B' and resid 150 through 164
      removed outlier: 3.763A  pdb=" N   PHE B 164 " --> pdb=" O   HIS B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 196
    Processing helix  chain 'B' and resid 207 through 214
    Processing helix  chain 'B' and resid 217 through 228
    Processing helix  chain 'B' and resid 236 through 247
    Processing helix  chain 'B' and resid 252 through 257
    Processing helix  chain 'B' and resid 270 through 283
      removed outlier: 3.759A  pdb=" N   ASP B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLN B 281 " --> pdb=" O   ASN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 306
      removed outlier: 3.905A  pdb=" N   ILE B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 343
      removed outlier: 3.715A  pdb=" N   SER B 320 " --> pdb=" O   PRO B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 353
      removed outlier: 3.522A  pdb=" N   ASP B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 364
    Processing helix  chain 'B' and resid 368 through 383
      Proline residue:  B 378  - end of helix
    Processing helix  chain 'B' and resid 386 through 395
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 3.900A  pdb=" N   GLY B 408 " --> pdb=" O   PHE B 405 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   SER B 409 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 427
      removed outlier: 4.351A  pdb=" N   HIS B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 436
      removed outlier: 3.603A  pdb=" N   LYS B 434 " --> pdb=" O   TYR B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 446
    Processing helix  chain 'B' and resid 477 through 482
      removed outlier: 3.779A  pdb=" N   VAL B 482 " --> pdb=" O   PHE B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 496
      removed outlier: 3.899A  pdb=" N   THR B 496 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 525
      removed outlier: 3.554A  pdb=" N   GLU B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 552
    Processing helix  chain 'B' and resid 560 through 568
      removed outlier: 3.657A  pdb=" N   TYR B 568 " --> pdb=" O   LEU B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 602
    Processing helix  chain 'B' and resid 603 through 609
    Processing helix  chain 'B' and resid 612 through 625
    Processing helix  chain 'B' and resid 628 through 637
    Processing helix  chain 'B' and resid 638 through 643
      removed outlier: 4.529A  pdb=" N   HIS B 641 " --> pdb=" O   THR B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 644 through 654
    Processing helix  chain 'B' and resid 664 through 669
    Processing helix  chain 'B' and resid 678 through 685
    Processing helix  chain 'B' and resid 692 through 698
    Processing helix  chain 'B' and resid 702 through 713
      removed outlier: 4.276A  pdb=" N   GLU B 706 " --> pdb=" O   LEU B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 727
    Processing helix  chain 'B' and resid 730 through 751
    Processing helix  chain 'B' and resid 776 through 792
    Processing helix  chain 'B' and resid 794 through 799
    Processing helix  chain 'B' and resid 804 through 807
      removed outlier: 3.705A  pdb=" N   GLN B 807 " --> pdb=" O   THR B 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 804 through 807'
    Processing helix  chain 'B' and resid 808 through 817
      removed outlier: 3.642A  pdb=" N   TYR B 812 " --> pdb=" O   ASN B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 860 through 865
      removed outlier: 3.538A  pdb=" N   GLY B 865 " --> pdb=" O   LYS B 862 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 872 through 889
      removed outlier: 3.555A  pdb=" N   VAL B 876 " --> pdb=" O   SER B 872 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASN B 881 " --> pdb=" O   LYS B 877 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   TYR B 882 " --> pdb=" O   LYS B 878 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 893 through 901
    Processing helix  chain 'B' and resid 901 through 906
    Processing helix  chain 'B' and resid 909 through 922
    Processing helix  chain 'B' and resid 926 through 940
    Processing helix  chain 'B' and resid 959 through 970
      removed outlier: 4.206A  pdb=" N   VAL B 963 " --> pdb=" O   LYS B 959 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE B 970 " --> pdb=" O   PHE B 966 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 980 through 1001
      removed outlier: 4.530A  pdb=" N   ALA B 984 " --> pdb=" O   ASN B 980 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1004 through 1009
    Processing helix  chain 'B' and resid 1043 through 1047
    Processing helix  chain 'B' and resid 1078 through 1088
    Processing helix  chain 'B' and resid 1127 through 1132
      removed outlier: 3.513A  pdb=" N   TYR B1131 " --> pdb=" O   ASP B1127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1168 through 1177
      removed outlier: 4.582A  pdb=" N   SER B1172 " --> pdb=" O   ILE B1168 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   SER B1173 " --> pdb=" O   MET B1169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1177 through 1186
    Processing helix  chain 'B' and resid 1207 through 1209
      No H-bonds generated for 'chain 'B' and resid 1207 through 1209'
    Processing helix  chain 'B' and resid 1229 through 1241
    Processing helix  chain 'B' and resid 1248 through 1262
    Processing helix  chain 'B' and resid 1264 through 1278
      removed outlier: 3.616A  pdb=" N   SER B1274 " --> pdb=" O   ILE B1270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1283 through 1297
    Processing helix  chain 'B' and resid 1306 through 1311
      removed outlier: 3.976A  pdb=" N   HIS B1311 " --> pdb=" O   GLU B1307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1312 through 1317
      removed outlier: 3.592A  pdb=" N   LEU B1315 " --> pdb=" O   LEU B1312 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN B1317 " --> pdb=" O   THR B1314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1340 through 1344
    Processing helix  chain 'B' and resid 1363 through 1365
      No H-bonds generated for 'chain 'B' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957
      removed outlier: 4.152A  pdb=" N   ASN B 758 " --> pdb=" O   TYR B   5 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 32
    Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35
      removed outlier: 3.821A  pdb=" N   LEU B  35 " --> pdb=" O   GLU B1357 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG B1359 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LEU B1203 " --> pdb=" O   ILE B1348 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   SER B1202 " --> pdb=" O   LEU B1214 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539
      removed outlier: 3.759A  pdb=" N   ALA B 538 " --> pdb=" O   TYR B 529 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   TYR B 529 " --> pdb=" O   ALA B 538 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840
      removed outlier: 3.874A  pdb=" N   ASP B 837 " --> pdb=" O   THR B 858 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   THR B 858 " --> pdb=" O   ASP B 837 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1051
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1106 through 1111
      removed outlier: 6.866A  pdb=" N   LYS B1107 " --> pdb=" O   PRO B1137 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER B1109 " --> pdb=" O   ASP B1135 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   ASP B1135 " --> pdb=" O   SER B1109 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY B1133 " --> pdb=" O   LEU B1111 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1167
      removed outlier: 3.730A  pdb=" N   GLU B1162 " --> pdb=" O   VAL B1145 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL B1145 " --> pdb=" O   GLU B1162 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TYR B1141 " --> pdb=" O   ILE B1166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326

    512 hydrogen bonds defined for protein.
    1467 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      125 hydrogen bonds
      242 hydrogen bond angles
      0 basepair planarities
      51 basepair parallelities
      93 stacking parallelities
  Total time for adding SS restraints: 3.01

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3110
        1.33 -     1.45: 3728
        1.45 -     1.57: 7575
        1.57 -     1.69: 290
        1.69 -     1.81: 44
  Bond restraints: 14747
  Sorted by residual:
  bond pdb=" C   PHE B 446 "
       pdb=" N   ARG B 447 "
    ideal  model  delta    sigma   weight residual
    1.332  1.359 -0.027 1.26e-02 6.30e+03 4.69e+00
  bond pdb=" CA  SER B1106 "
       pdb=" CB  SER B1106 "
    ideal  model  delta    sigma   weight residual
    1.530  1.489  0.041 1.93e-02 2.68e+03 4.43e+00
  bond pdb=" N   ARG B1333 "
       pdb=" CA  ARG B1333 "
    ideal  model  delta    sigma   weight residual
    1.456  1.481 -0.025 1.22e-02 6.72e+03 4.33e+00
  bond pdb=" N   SER B1106 "
       pdb=" CA  SER B1106 "
    ideal  model  delta    sigma   weight residual
    1.458  1.477 -0.019 1.27e-02 6.20e+03 2.14e+00
  bond pdb=" CB  VAL B 452 "
       pdb=" CG1 VAL B 452 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.01e+00
  ... (remaining 14742 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 19987
        1.18 -     2.36: 465
        2.36 -     3.54: 71
        3.54 -     4.72: 7
        4.72 -     5.90: 6
  Bond angle restraints: 20536
  Sorted by residual:
  angle pdb=" O   PHE B 446 "
        pdb=" C   PHE B 446 "
        pdb=" N   ARG B 447 "
      ideal   model   delta    sigma   weight residual
     122.96  128.75   -5.79 1.26e+00 6.30e-01 2.11e+01
  angle pdb=" CA  PHE B 446 "
        pdb=" C   PHE B 446 "
        pdb=" N   ARG B 447 "
      ideal   model   delta    sigma   weight residual
     116.43  110.53    5.90 1.37e+00 5.33e-01 1.86e+01
  angle pdb=" C   PHE B 446 "
        pdb=" N   ARG B 447 "
        pdb=" CA  ARG B 447 "
      ideal   model   delta    sigma   weight residual
     122.39  116.69    5.70 1.48e+00 4.57e-01 1.48e+01
  angle pdb=" CA  PHE B1105 "
        pdb=" C   PHE B1105 "
        pdb=" N   SER B1106 "
      ideal   model   delta    sigma   weight residual
     117.63  114.39    3.24 1.25e+00 6.40e-01 6.72e+00
  angle pdb=" CA  ARG B1333 "
        pdb=" C   ARG B1333 "
        pdb=" O   ARG B1333 "
      ideal   model   delta    sigma   weight residual
     121.16  118.52    2.64 1.12e+00 7.97e-01 5.57e+00
  ... (remaining 20531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.93: 8456
       35.93 -    71.86: 457
       71.86 -   107.78: 18
      107.78 -   143.71: 1
      143.71 -   179.64: 2
  Dihedral angle restraints: 8934
    sinusoidal: 4944
      harmonic: 3990
  Sorted by residual:
  dihedral pdb=" C4'  DA D  -2 "
           pdb=" C3'  DA D  -2 "
           pdb=" O3'  DA D  -2 "
           pdb=" P    DT D  -1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.64 -179.64     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'   U A  80 "
           pdb=" C3'   U A  80 "
           pdb=" O3'   U A  80 "
           pdb=" P     G A  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   27.05 -167.05     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'  DC C   5 "
           pdb=" C3'  DC C   5 "
           pdb=" O3'  DC C   5 "
           pdb=" P    DT C   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   81.09  138.91     1      3.50e+01 8.16e-04 1.37e+01
  ... (remaining 8931 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1763
       0.035 -    0.069: 447
       0.069 -    0.104: 100
       0.104 -    0.138: 30
       0.138 -    0.173: 2
  Chirality restraints: 2342
  Sorted by residual:
  chirality pdb=" C1'   A A  12 "
            pdb=" O4'   A A  12 "
            pdb=" C2'   A A  12 "
            pdb=" N9    A A  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" C2'   G A  16 "
            pdb=" C3'   G A  16 "
            pdb=" O2'   G A  16 "
            pdb=" C1'   G A  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.59   -0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" C1'   A A  41 "
            pdb=" O4'   A A  41 "
            pdb=" C2'   A A  41 "
            pdb=" N9    A A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.32    0.14 2.00e-01 2.50e+01 4.75e-01
  ... (remaining 2339 not shown)

  Planarity restraints: 2093
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A  13 "   -0.025 2.00e-02 2.50e+03   1.27e-02 3.64e+00
        pdb=" N1    U A  13 "    0.027 2.00e-02 2.50e+03
        pdb=" C2    U A  13 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    U A  13 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U A  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    U A  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" O4    U A  13 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    U A  13 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U A  13 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 454 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.31e+00
        pdb=" C   PRO B 454 "    0.031 2.00e-02 2.50e+03
        pdb=" O   PRO B 454 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU B 455 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A  12 "   -0.023 2.00e-02 2.50e+03   1.05e-02 3.06e+00
        pdb=" N9    A A  12 "    0.025 2.00e-02 2.50e+03
        pdb=" C8    A A  12 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A A  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A A  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A A  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A A  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    A A  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A A  12 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A A  12 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A A  12 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2090 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2437
        2.77 -     3.30: 13375
        3.30 -     3.83: 24711
        3.83 -     4.37: 28632
        4.37 -     4.90: 45023
  Nonbonded interactions: 114178
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 474 "
            pdb=" OD1 ASN B 477 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   LEU B 551 "
            pdb=" OG1 THR B 555 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   HIS B 799 "
            pdb=" OH  TYR B 815 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O2'   U A  56 "
            pdb=" N2    G A  58 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OE1 GLU B1357 "
            pdb=" NH1 ARG B1359 "
     model   vdw
     2.265 3.120
  ... (remaining 114173 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:             6.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.710
  Find NCS groups from input model:        0.060
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14747  Z= 0.137
  Angle     :  0.451   5.903  20536  Z= 0.255
  Chirality :  0.034   0.173   2342
  Planarity :  0.003   0.031   2093
  Dihedral  : 17.564 179.639   6354
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  4.28 %
    Favored  : 93.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.06 (0.23), residues: 1353
  helix:  1.93 (0.21), residues: 656
  sheet: -0.18 (0.48), residues: 118
  loop : -0.52 (0.24), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 165 
 TYR   0.011   0.001   TYR B 155 
 PHE   0.009   0.001   PHE B1276 
 TRP   0.009   0.001   TRP B 464 
 HIS   0.003   0.001   HIS B1349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (14747)
  covalent geometry    : angle       0.45094 (20536)
  hydrogen bonds       : bond        0.15410 (  637)
  hydrogen bonds       : angle       5.43938 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.391 
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: B  174 LEU cc_start: 0.9221 (pp) cc_final: 0.8865 (tp)
REVERT: B  534 MET cc_start: 0.6025 (mtp) cc_final: 0.5743 (ptp)
REVERT: B  703 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8935 (p)
REVERT: B  727 LEU cc_start: 0.8780 (mt) cc_final: 0.8235 (mt)
REVERT: B  734 LYS cc_start: 0.9386 (mtmt) cc_final: 0.9087 (mtmt)
REVERT: B  782 LYS cc_start: 0.9800 (ttmt) cc_final: 0.9568 (ptmm)
REVERT: B  815 TYR cc_start: 0.9516 (m-80) cc_final: 0.8945 (m-80)
REVERT: B 1004 LEU cc_start: 0.8927 (mt) cc_final: 0.8512 (mt)
REVERT: B 1099 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8185 (mt-10)
REVERT: B 1333 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8684 (ptt180)
  outliers start: 25
  outliers final: 6
  residues processed: 156
  average time/residue: 0.1336
  time to fit residues: 29.2628
Evaluate side-chains
  83 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  450 TYR
Chi-restraints excluded: chain B residue  539 PHE
Chi-restraints excluded: chain B residue  703 THR
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue 1018 VAL
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 415 HIS
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 612 ASN
B 698 HIS
B 826 GLN
** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 885 GLN
** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1041 ASN
B1305 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.048913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.034419 restraints weight = 109280.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.035704 restraints weight = 53911.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.036406 restraints weight = 35293.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.036885 restraints weight = 27940.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.037178 restraints weight = 24311.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14747  Z= 0.242
  Angle     :  0.600  10.618  20536  Z= 0.317
  Chirality :  0.037   0.184   2342
  Planarity :  0.004   0.045   2093
  Dihedral  : 21.052 177.736   3485
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.21 %
    Favored  : 88.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.23), residues: 1353
  helix:  1.77 (0.21), residues: 678
  sheet:  0.37 (0.54), residues: 95
  loop : -0.65 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 864 
 TYR   0.029   0.002   TYR B 823 
 PHE   0.014   0.001   PHE B 518 
 TRP   0.012   0.002   TRP B  18 
 HIS   0.008   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (14747)
  covalent geometry    : angle       0.59962 (20536)
  hydrogen bonds       : bond        0.05129 (  637)
  hydrogen bonds       : angle       4.51647 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.481 
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: B  495 MET cc_start: 0.7645 (tpt) cc_final: 0.7427 (tpt)
REVERT: B  517 TYR cc_start: 0.9441 (m-80) cc_final: 0.9191 (m-80)
REVERT: B  703 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9008 (p)
REVERT: B  727 LEU cc_start: 0.8569 (mt) cc_final: 0.8058 (mt)
REVERT: B  815 TYR cc_start: 0.9574 (m-80) cc_final: 0.9046 (m-80)
REVERT: B 1021 MET cc_start: 0.8742 (mpp) cc_final: 0.8281 (mpp)
REVERT: B 1099 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8258 (mt-10)
REVERT: B 1169 MET cc_start: 0.8908 (mtp) cc_final: 0.8333 (mmm)
REVERT: B 1333 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8409 (ptt180)
REVERT: B 1355 LEU cc_start: 0.9510 (mt) cc_final: 0.8821 (mm)
REVERT: B 1357 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8464 (mp0)
  outliers start: 26
  outliers final: 15
  residues processed: 94
  average time/residue: 0.1121
  time to fit residues: 16.0560
Evaluate side-chains
  75 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  539 PHE
Chi-restraints excluded: chain B residue  703 THR
Chi-restraints excluded: chain B residue  740 THR
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue 1018 VAL
Chi-restraints excluded: chain B residue 1156 LYS
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Chi-restraints excluded: chain B residue 1348 ILE
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 108 optimal weight:    6.9990
   chunk 84 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 112 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 94 optimal weight:   40.0000
   chunk 11 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 511 HIS
B 556 ASN
** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.047074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.032756 restraints weight = 113476.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.033962 restraints weight = 55389.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.034672 restraints weight = 36461.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.035028 restraints weight = 28754.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.035299 restraints weight = 25513.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  14747  Z= 0.293
  Angle     :  0.642  11.316  20536  Z= 0.341
  Chirality :  0.039   0.210   2342
  Planarity :  0.004   0.056   2093
  Dihedral  : 21.214 175.567   3483
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.25 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.22), residues: 1353
  helix:  1.41 (0.20), residues: 669
  sheet:  0.42 (0.54), residues: 93
  loop : -0.71 (0.24), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 165 
 TYR   0.015   0.002   TYR B1141 
 PHE   0.014   0.002   PHE B 372 
 TRP   0.013   0.002   TRP B 659 
 HIS   0.009   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 (14747)
  covalent geometry    : angle       0.64162 (20536)
  hydrogen bonds       : bond        0.05671 (  637)
  hydrogen bonds       : angle       4.71533 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 61
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  450 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7960 (m-10)
REVERT: B  517 TYR cc_start: 0.9497 (m-80) cc_final: 0.9204 (m-80)
REVERT: B  534 MET cc_start: 0.6761 (ttm) cc_final: 0.5622 (ptm)
REVERT: B  727 LEU cc_start: 0.8442 (mt) cc_final: 0.8030 (mt)
REVERT: B  759 ILE cc_start: 0.9392 (mt) cc_final: 0.9181 (tp)
REVERT: B  815 TYR cc_start: 0.9609 (m-80) cc_final: 0.9101 (m-80)
REVERT: B 1021 MET cc_start: 0.8827 (mpp) cc_final: 0.8397 (mpp)
REVERT: B 1099 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8144 (mt-10)
REVERT: B 1169 MET cc_start: 0.8944 (mtp) cc_final: 0.8054 (mmm)
REVERT: B 1333 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8281 (ptt180)
REVERT: B 1355 LEU cc_start: 0.9477 (mt) cc_final: 0.8922 (mm)
REVERT: B 1357 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8220 (mp0)
  outliers start: 32
  outliers final: 19
  residues processed: 90
  average time/residue: 0.1277
  time to fit residues: 16.9732
Evaluate side-chains
  77 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  450 TYR
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  539 PHE
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  721 HIS
Chi-restraints excluded: chain B residue  740 THR
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue 1004 LEU
Chi-restraints excluded: chain B residue 1010 TYR
Chi-restraints excluded: chain B residue 1018 VAL
Chi-restraints excluded: chain B residue 1037 PHE
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1348 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 100 optimal weight:    7.9990
   chunk 146 optimal weight:    6.9990
   chunk 127 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 89 optimal weight:    0.6980
   chunk 67 optimal weight:    6.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 412 HIS
** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.047447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.033068 restraints weight = 112913.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.034275 restraints weight = 55062.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.035011 restraints weight = 36336.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.035405 restraints weight = 28633.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.035556 restraints weight = 25237.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14747  Z= 0.207
  Angle     :  0.561  12.899  20536  Z= 0.298
  Chirality :  0.037   0.210   2342
  Planarity :  0.003   0.051   2093
  Dihedral  : 21.137 176.125   3482
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.49 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.22), residues: 1353
  helix:  1.52 (0.20), residues: 672
  sheet:  0.55 (0.56), residues: 88
  loop : -0.69 (0.24), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 165 
 TYR   0.019   0.001   TYR B 988 
 PHE   0.010   0.001   PHE B 372 
 TRP   0.009   0.001   TRP B  18 
 HIS   0.006   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (14747)
  covalent geometry    : angle       0.56079 (20536)
  hydrogen bonds       : bond        0.04448 (  637)
  hydrogen bonds       : angle       4.37605 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 60
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 MET cc_start: 0.8382 (mmt) cc_final: 0.7743 (mmm)
REVERT: B  517 TYR cc_start: 0.9483 (m-80) cc_final: 0.9224 (m-80)
REVERT: B  534 MET cc_start: 0.6604 (ttm) cc_final: 0.5474 (ptm)
REVERT: B  727 LEU cc_start: 0.8558 (mt) cc_final: 0.8025 (mt)
REVERT: B  815 TYR cc_start: 0.9552 (m-80) cc_final: 0.9048 (m-80)
REVERT: B 1021 MET cc_start: 0.8872 (mpp) cc_final: 0.8329 (mpp)
REVERT: B 1099 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8142 (mt-10)
REVERT: B 1169 MET cc_start: 0.8957 (mtp) cc_final: 0.8741 (tpt)
REVERT: B 1219 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7135 (mt-10)
REVERT: B 1333 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8272 (ptt180)
REVERT: B 1355 LEU cc_start: 0.9470 (mt) cc_final: 0.8928 (mm)
REVERT: B 1357 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8233 (mp0)
  outliers start: 26
  outliers final: 20
  residues processed: 83
  average time/residue: 0.1251
  time to fit residues: 15.6404
Evaluate side-chains
  76 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  539 PHE
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  721 HIS
Chi-restraints excluded: chain B residue  740 THR
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue  879 MET
Chi-restraints excluded: chain B residue 1010 TYR
Chi-restraints excluded: chain B residue 1018 VAL
Chi-restraints excluded: chain B residue 1037 PHE
Chi-restraints excluded: chain B residue 1156 LYS
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1348 ILE
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 119 optimal weight:    0.5980
   chunk 141 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0020
   chunk 72 optimal weight:    6.9990
   chunk 117 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 132 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 92 optimal weight:   20.0000
   chunk 122 optimal weight:    3.9990
   overall best weight:    2.7194

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

Flipped N/Q/H residues before XYZ refinement:
** B 990 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 = 0.3326 r_free = 0.3326 target = 0.047974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.033652 restraints weight = 111311.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.034886 restraints weight = 54352.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.035609 restraints weight = 35888.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.036021 restraints weight = 28211.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.036306 restraints weight = 24678.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14747  Z= 0.143
  Angle     :  0.520   9.428  20536  Z= 0.274
  Chirality :  0.036   0.215   2342
  Planarity :  0.003   0.051   2093
  Dihedral  : 20.975 176.144   3482
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.16 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.23), residues: 1353
  helix:  1.71 (0.21), residues: 673
  sheet:  0.52 (0.56), residues: 88
  loop : -0.53 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 165 
 TYR   0.008   0.001   TYR B 823 
 PHE   0.007   0.001   PHE B 846 
 TRP   0.005   0.001   TRP B 476 
 HIS   0.005   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (14747)
  covalent geometry    : angle       0.51968 (20536)
  hydrogen bonds       : bond        0.03781 (  637)
  hydrogen bonds       : angle       4.14692 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 61
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 MET cc_start: 0.9482 (mmm) cc_final: 0.9144 (mmm)
REVERT: B  383 MET cc_start: 0.8401 (mmt) cc_final: 0.7775 (mmm)
REVERT: B  517 TYR cc_start: 0.9448 (m-80) cc_final: 0.9230 (m-80)
REVERT: B  534 MET cc_start: 0.6414 (ttm) cc_final: 0.5292 (ptm)
REVERT: B  722 GLU cc_start: 0.9659 (mt-10) cc_final: 0.9408 (pt0)
REVERT: B  727 LEU cc_start: 0.8555 (mt) cc_final: 0.8136 (mt)
REVERT: B  815 TYR cc_start: 0.9514 (m-80) cc_final: 0.9017 (m-80)
REVERT: B 1021 MET cc_start: 0.8800 (mpp) cc_final: 0.8273 (mpp)
REVERT: B 1099 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: B 1169 MET cc_start: 0.8920 (mtp) cc_final: 0.8603 (tpp)
REVERT: B 1219 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7088 (mt-10)
REVERT: B 1333 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8314 (ptt180)
REVERT: B 1348 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9058 (tt)
REVERT: B 1355 LEU cc_start: 0.9452 (mt) cc_final: 0.8901 (mm)
REVERT: B 1357 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8245 (mp0)
  outliers start: 28
  outliers final: 18
  residues processed: 85
  average time/residue: 0.1176
  time to fit residues: 15.0539
Evaluate side-chains
  77 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  539 PHE
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  740 THR
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue  879 MET
Chi-restraints excluded: chain B residue  958 LEU
Chi-restraints excluded: chain B residue 1004 LEU
Chi-restraints excluded: chain B residue 1010 TYR
Chi-restraints excluded: chain B residue 1037 PHE
Chi-restraints excluded: chain B residue 1156 LYS
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1348 ILE
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 133 optimal weight:    0.0870
   chunk 105 optimal weight:    2.9990
   chunk 91 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 15 optimal weight:    0.2980
   chunk 85 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 104 optimal weight:    6.9990
   chunk 124 optimal weight:    9.9990
   chunk 125 optimal weight:    0.3980
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
B 863 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.049104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.035022 restraints weight = 107736.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.036259 restraints weight = 52420.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.036975 restraints weight = 34416.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.037440 restraints weight = 27038.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.037697 restraints weight = 23382.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  14747  Z= 0.097
  Angle     :  0.493   9.792  20536  Z= 0.258
  Chirality :  0.035   0.193   2342
  Planarity :  0.003   0.050   2093
  Dihedral  : 20.759 177.037   3481
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.82 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.23), residues: 1353
  helix:  1.86 (0.21), residues: 673
  sheet:  0.59 (0.55), residues: 88
  loop : -0.40 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 864 
 TYR   0.037   0.001   TYR B 823 
 PHE   0.007   0.001   PHE B1235 
 TRP   0.003   0.001   TRP B1126 
 HIS   0.005   0.001   HIS B 723 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (14747)
  covalent geometry    : angle       0.49296 (20536)
  hydrogen bonds       : bond        0.03132 (  637)
  hydrogen bonds       : angle       3.89621 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 MET cc_start: 0.9456 (mmm) cc_final: 0.9197 (mmm)
REVERT: B  383 MET cc_start: 0.8395 (mmt) cc_final: 0.7762 (mmm)
REVERT: B  534 MET cc_start: 0.6094 (ttm) cc_final: 0.5008 (ptm)
REVERT: B  722 GLU cc_start: 0.9662 (mt-10) cc_final: 0.9462 (pt0)
REVERT: B  727 LEU cc_start: 0.8696 (mt) cc_final: 0.8069 (mt)
REVERT: B  751 MET cc_start: 0.8901 (tpp) cc_final: 0.8460 (ttm)
REVERT: B  815 TYR cc_start: 0.9443 (m-80) cc_final: 0.8965 (m-80)
REVERT: B  879 MET cc_start: 0.6417 (mtp) cc_final: 0.6120 (ptp)
REVERT: B 1021 MET cc_start: 0.8755 (mpp) cc_final: 0.8234 (mpp)
REVERT: B 1099 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8198 (tt0)
REVERT: B 1169 MET cc_start: 0.8906 (mtp) cc_final: 0.8622 (tpp)
REVERT: B 1213 MET cc_start: 0.7039 (tpp) cc_final: 0.6640 (tpp)
REVERT: B 1219 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7014 (mt-10)
REVERT: B 1333 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8361 (ptt180)
REVERT: B 1348 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9018 (tt)
REVERT: B 1355 LEU cc_start: 0.9436 (mt) cc_final: 0.8885 (mm)
REVERT: B 1357 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8188 (mp0)
  outliers start: 19
  outliers final: 7
  residues processed: 85
  average time/residue: 0.1204
  time to fit residues: 15.3454
Evaluate side-chains
  68 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  740 THR
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  958 LEU
Chi-restraints excluded: chain B residue  965 ASP
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1219 GLU
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Chi-restraints excluded: chain B residue 1348 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 56 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 146 optimal weight:    9.9990
   chunk 60 optimal weight:    0.3980
   chunk 95 optimal weight:   20.0000
   chunk 94 optimal weight:    0.9980
   chunk 137 optimal weight:    4.9990
   overall best weight:    1.6584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.048935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.034859 restraints weight = 108852.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.036107 restraints weight = 53422.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.036847 restraints weight = 35026.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.037295 restraints weight = 27397.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.037520 restraints weight = 23761.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  14747  Z= 0.111
  Angle     :  0.516  11.583  20536  Z= 0.265
  Chirality :  0.035   0.180   2342
  Planarity :  0.003   0.051   2093
  Dihedral  : 20.694 177.057   3478
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.98 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.23), residues: 1353
  helix:  1.83 (0.21), residues: 674
  sheet:  0.56 (0.56), residues: 88
  loop : -0.34 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 778 
 TYR   0.017   0.001   TYR B 823 
 PHE   0.008   0.001   PHE B1276 
 TRP   0.003   0.001   TRP B 476 
 HIS   0.004   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (14747)
  covalent geometry    : angle       0.51555 (20536)
  hydrogen bonds       : bond        0.03347 (  637)
  hydrogen bonds       : angle       3.93795 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.505 
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: B   90 MET cc_start: 0.9442 (mmm) cc_final: 0.9172 (mmm)
REVERT: B  161 MET cc_start: 0.9184 (ptm) cc_final: 0.8920 (ptp)
REVERT: B  383 MET cc_start: 0.8403 (mmt) cc_final: 0.7796 (mmm)
REVERT: B  534 MET cc_start: 0.6145 (ttm) cc_final: 0.5007 (ptm)
REVERT: B  727 LEU cc_start: 0.8680 (mt) cc_final: 0.8049 (mt)
REVERT: B  751 MET cc_start: 0.8946 (tpp) cc_final: 0.8490 (ttt)
REVERT: B  813 LEU cc_start: 0.9858 (mt) cc_final: 0.9628 (tp)
REVERT: B  815 TYR cc_start: 0.9461 (m-80) cc_final: 0.9006 (m-80)
REVERT: B  965 ASP cc_start: 0.9512 (OUTLIER) cc_final: 0.9081 (m-30)
REVERT: B 1021 MET cc_start: 0.8737 (mpp) cc_final: 0.8244 (mpp)
REVERT: B 1099 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8317 (tt0)
REVERT: B 1169 MET cc_start: 0.8915 (mtp) cc_final: 0.8608 (tpp)
REVERT: B 1219 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7037 (mt-10)
REVERT: B 1333 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8329 (ptt180)
REVERT: B 1348 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9017 (tt)
  outliers start: 20
  outliers final: 12
  residues processed: 77
  average time/residue: 0.1082
  time to fit residues: 13.0517
Evaluate side-chains
  73 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  721 HIS
Chi-restraints excluded: chain B residue  740 THR
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue  939 MET
Chi-restraints excluded: chain B residue  958 LEU
Chi-restraints excluded: chain B residue  965 ASP
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1219 GLU
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1348 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 125 optimal weight:    0.6980
   chunk 141 optimal weight:    6.9990
   chunk 83 optimal weight:   20.0000
   chunk 137 optimal weight:    7.9990
   chunk 123 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 36 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
B 415 HIS
** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.048158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.033980 restraints weight = 110887.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.035197 restraints weight = 54892.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.035938 restraints weight = 36133.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.036340 restraints weight = 28297.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.036622 restraints weight = 24766.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14747  Z= 0.159
  Angle     :  0.544  10.828  20536  Z= 0.281
  Chirality :  0.036   0.175   2342
  Planarity :  0.003   0.049   2093
  Dihedral  : 20.728 176.661   3478
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.47 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.23), residues: 1353
  helix:  1.80 (0.21), residues: 674
  sheet:  0.43 (0.57), residues: 88
  loop : -0.36 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1359 
 TYR   0.014   0.001   TYR B1010 
 PHE   0.008   0.001   PHE B 372 
 TRP   0.009   0.001   TRP B  18 
 HIS   0.005   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (14747)
  covalent geometry    : angle       0.54423 (20536)
  hydrogen bonds       : bond        0.03830 (  637)
  hydrogen bonds       : angle       4.03969 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 MET cc_start: 0.9460 (mmm) cc_final: 0.9183 (mmm)
REVERT: B  383 MET cc_start: 0.8434 (mmt) cc_final: 0.7853 (mmm)
REVERT: B  534 MET cc_start: 0.6251 (ttm) cc_final: 0.5057 (ptm)
REVERT: B  727 LEU cc_start: 0.8690 (mt) cc_final: 0.8098 (mt)
REVERT: B  813 LEU cc_start: 0.9864 (mt) cc_final: 0.9640 (tp)
REVERT: B  815 TYR cc_start: 0.9502 (m-80) cc_final: 0.9041 (m-80)
REVERT: B  848 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7910 (tptp)
REVERT: B 1021 MET cc_start: 0.8791 (mpp) cc_final: 0.8286 (mpp)
REVERT: B 1043 MET cc_start: 0.8675 (tmm) cc_final: 0.8409 (tmm)
REVERT: B 1099 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8163 (mt-10)
REVERT: B 1108 GLU cc_start: 0.9085 (pm20) cc_final: 0.8852 (pm20)
REVERT: B 1169 MET cc_start: 0.8913 (mtp) cc_final: 0.8624 (tpp)
REVERT: B 1213 MET cc_start: 0.7105 (tpp) cc_final: 0.6777 (tpp)
REVERT: B 1219 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7035 (mt-10)
REVERT: B 1333 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8321 (ptt180)
  outliers start: 23
  outliers final: 17
  residues processed: 73
  average time/residue: 0.1080
  time to fit residues: 12.3604
Evaluate side-chains
  74 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  740 THR
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue  879 MET
Chi-restraints excluded: chain B residue  939 MET
Chi-restraints excluded: chain B residue  958 LEU
Chi-restraints excluded: chain B residue 1004 LEU
Chi-restraints excluded: chain B residue 1073 VAL
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1190 VAL
Chi-restraints excluded: chain B residue 1219 GLU
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Chi-restraints excluded: chain B residue 1342 VAL
Chi-restraints excluded: chain B residue 1352 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 131 optimal weight:    6.9990
   chunk 134 optimal weight:    9.9990
   chunk 46 optimal weight:    9.9990
   chunk 146 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 420 HIS
** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.047975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.033875 restraints weight = 111104.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.035089 restraints weight = 54292.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.035817 restraints weight = 35676.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.036221 restraints weight = 27922.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.036523 restraints weight = 24443.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14747  Z= 0.156
  Angle     :  0.547  12.673  20536  Z= 0.283
  Chirality :  0.035   0.173   2342
  Planarity :  0.003   0.048   2093
  Dihedral  : 20.734 176.047   3478
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.56 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.23), residues: 1353
  helix:  1.72 (0.21), residues: 672
  sheet:  0.34 (0.58), residues: 88
  loop : -0.32 (0.25), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 778 
 TYR   0.017   0.001   TYR B1010 
 PHE   0.007   0.001   PHE B 966 
 TRP   0.007   0.001   TRP B  18 
 HIS   0.005   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (14747)
  covalent geometry    : angle       0.54735 (20536)
  hydrogen bonds       : bond        0.03858 (  637)
  hydrogen bonds       : angle       4.07299 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   86 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8681 (t80)
REVERT: B   90 MET cc_start: 0.9452 (mmm) cc_final: 0.9116 (mmm)
REVERT: B  383 MET cc_start: 0.8415 (mmt) cc_final: 0.7835 (mmm)
REVERT: B  534 MET cc_start: 0.6154 (ttm) cc_final: 0.4938 (ptm)
REVERT: B  727 LEU cc_start: 0.8709 (mt) cc_final: 0.8119 (mt)
REVERT: B  751 MET cc_start: 0.8985 (tpp) cc_final: 0.8730 (ttt)
REVERT: B  813 LEU cc_start: 0.9867 (mt) cc_final: 0.9651 (tp)
REVERT: B  815 TYR cc_start: 0.9524 (m-80) cc_final: 0.9051 (m-80)
REVERT: B  848 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7952 (tptp)
REVERT: B 1021 MET cc_start: 0.8765 (mpp) cc_final: 0.8242 (mpp)
REVERT: B 1089 MET cc_start: 0.9086 (mmm) cc_final: 0.8878 (mmm)
REVERT: B 1099 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8169 (mt-10)
REVERT: B 1169 MET cc_start: 0.8893 (mtp) cc_final: 0.8616 (tpp)
REVERT: B 1219 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7017 (mt-10)
REVERT: B 1333 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8265 (ptt180)
  outliers start: 20
  outliers final: 15
  residues processed: 69
  average time/residue: 0.1173
  time to fit residues: 12.3811
Evaluate side-chains
  72 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue  879 MET
Chi-restraints excluded: chain B residue  939 MET
Chi-restraints excluded: chain B residue  958 LEU
Chi-restraints excluded: chain B residue 1004 LEU
Chi-restraints excluded: chain B residue 1073 VAL
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1190 VAL
Chi-restraints excluded: chain B residue 1219 GLU
Chi-restraints excluded: chain B residue 1313 PHE
Chi-restraints excluded: chain B residue 1333 ARG
Chi-restraints excluded: chain B residue 1342 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 95 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   overall best weight:    1.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.049277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.035206 restraints weight = 110229.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.036488 restraints weight = 53740.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.037224 restraints weight = 35007.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.037671 restraints weight = 27332.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.037907 restraints weight = 23745.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  14747  Z= 0.101
  Angle     :  0.513  10.792  20536  Z= 0.264
  Chirality :  0.035   0.170   2342
  Planarity :  0.003   0.048   2093
  Dihedral  : 20.582 175.893   3478
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 15.13 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.23), residues: 1353
  helix:  1.81 (0.21), residues: 673
  sheet:  0.64 (0.62), residues: 76
  loop : -0.24 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 778 
 TYR   0.011   0.001   TYR B 823 
 PHE   0.006   0.001   PHE B1258 
 TRP   0.008   0.001   TRP B  18 
 HIS   0.004   0.001   HIS B1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (14747)
  covalent geometry    : angle       0.51346 (20536)
  hydrogen bonds       : bond        0.03178 (  637)
  hydrogen bonds       : angle       3.91023 ( 1709)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.420 
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: B   86 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8702 (t80)
REVERT: B   90 MET cc_start: 0.9427 (mmm) cc_final: 0.9128 (mmm)
REVERT: B  383 MET cc_start: 0.8410 (mmt) cc_final: 0.7846 (mmm)
REVERT: B  534 MET cc_start: 0.6094 (ttm) cc_final: 0.4962 (ptm)
REVERT: B  727 LEU cc_start: 0.8650 (mt) cc_final: 0.8038 (mt)
REVERT: B  813 LEU cc_start: 0.9864 (mt) cc_final: 0.9644 (tp)
REVERT: B  815 TYR cc_start: 0.9450 (m-80) cc_final: 0.9030 (m-80)
REVERT: B  879 MET cc_start: 0.6874 (mtp) cc_final: 0.6335 (ptp)
REVERT: B 1099 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8039 (pt0)
REVERT: B 1169 MET cc_start: 0.8864 (mtp) cc_final: 0.8587 (tpp)
REVERT: B 1219 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7011 (mt-10)
REVERT: B 1333 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8299 (ptt180)
  outliers start: 11
  outliers final: 7
  residues processed: 65
  average time/residue: 0.1186
  time to fit residues: 11.9460
Evaluate side-chains
  65 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  791 LEU
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  842 VAL
Chi-restraints excluded: chain B residue  958 LEU
Chi-restraints excluded: chain B residue 1145 VAL
Chi-restraints excluded: chain B residue 1219 GLU
Chi-restraints excluded: chain B residue 1333 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 102 optimal weight:   30.0000
   chunk 106 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 138 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 930 HIS
B1297 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.047288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.033116 restraints weight = 113986.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.034313 restraints weight = 55915.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.034969 restraints weight = 36973.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.035413 restraints weight = 29425.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.035581 restraints weight = 25634.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.4515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  14747  Z= 0.228
  Angle     :  0.603  12.033  20536  Z= 0.318
  Chirality :  0.037   0.165   2342
  Planarity :  0.004   0.047   2093
  Dihedral  : 20.838 175.162   3476
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.88 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.23), residues: 1353
  helix:  1.59 (0.20), residues: 677
  sheet:  0.59 (0.62), residues: 76
  loop : -0.37 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  71 
 TYR   0.018   0.002   TYR B 451 
 PHE   0.014   0.001   PHE B 372 
 TRP   0.009   0.002   TRP B 659 
 HIS   0.007   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (14747)
  covalent geometry    : angle       0.60295 (20536)
  hydrogen bonds       : bond        0.04919 (  637)
  hydrogen bonds       : angle       4.22923 ( 1709)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2501.76 seconds
wall clock time: 43 minutes 56.68 seconds (2636.68 seconds total)