Starting phenix.real_space_refine
on Tue Nov 18 09:01:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z1g_39727/11_2025/8z1g_39727.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z1g_39727/11_2025/8z1g_39727.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z1g_39727/11_2025/8z1g_39727.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z1g_39727/11_2025/8z1g_39727.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z1g_39727/11_2025/8z1g_39727.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z1g_39727/11_2025/8z1g_39727.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      69      5.49       5
     S      38      5.16       5
     C    4066      2.51       5
     N    1207      2.21       5
     O    1463      1.98       5
     H    6138      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12983
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "T"
      Number of atoms: 2187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 2187
          Classifications: {'RNA': 68}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 14, 'rna3p': 53}
    Chain: "A"
      Number of atoms: 10789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 688, 10789
          Classifications: {'peptide': 688}
          Link IDs: {'PTRANS': 41, 'TRANS': 646}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 7
          Unusual residues: {' ZN': 2, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.72, per 1000 atoms: 0.21
  Number of scatterers: 12983
  At special positions: 0
  Unit cell: (68.38, 94.154, 128.344, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      38     16.00
     P      69     15.00
     O    1463      8.00
     N    1207      7.00
     C    4066      6.00
     H    6138      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 283.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" ND1 HIS A 548 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 546 "
        pdb="ZN    ZN A 901 " - pdb="ZN    ZN A 902 "
      pdb="  ZN A 902 "
        pdb="ZN    ZN A 902 " - pdb=" NE2 HIS A 551 "
        pdb="ZN    ZN A 902 " - pdb=" NE2 HIS A 724 "


  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1292

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 7 sheets defined
      39.2% alpha, 14.2% beta
      15 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 2.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 98
    Processing helix  chain 'A' and resid 114 through 119
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 143 through 156
      removed outlier: 3.669A  pdb=" N   TYR A 147 " --> pdb=" O   GLN A 143 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   PHE A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
      removed outlier: 3.848A  pdb=" N   MET A 262 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.886A  pdb=" N   ILE A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 296
      removed outlier: 3.502A  pdb=" N   GLU A 295 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 315
      No H-bonds generated for 'chain 'A' and resid 313 through 315'
    Processing helix  chain 'A' and resid 316 through 323
    Processing helix  chain 'A' and resid 324 through 330
      removed outlier: 3.933A  pdb=" N   ARG A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   TYR A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 351 through 359
    Processing helix  chain 'A' and resid 360 through 362
      No H-bonds generated for 'chain 'A' and resid 360 through 362'
    Processing helix  chain 'A' and resid 379 through 391
      removed outlier: 3.618A  pdb=" N   HIS A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 452
      removed outlier: 3.660A  pdb=" N   PHE A 446 " --> pdb=" O   ASN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 468
    Processing helix  chain 'A' and resid 520 through 529
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 548 through 553
      removed outlier: 3.764A  pdb=" N   HIS A 552 " --> pdb=" O   HIS A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 570
    Processing helix  chain 'A' and resid 581 through 591
      removed outlier: 3.931A  pdb=" N   LYS A 585 " --> pdb=" O   PRO A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 600
      No H-bonds generated for 'chain 'A' and resid 598 through 600'
    Processing helix  chain 'A' and resid 623 through 629
    Processing helix  chain 'A' and resid 693 through 701
    Processing helix  chain 'A' and resid 704 through 716
      removed outlier: 3.585A  pdb=" N   ASN A 716 " --> pdb=" O   GLY A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 730
      removed outlier: 3.612A  pdb=" N   ALA A 730 " --> pdb=" O   GLN A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 757
      removed outlier: 3.548A  pdb=" N   PHE A 757 " --> pdb=" O   PHE A 754 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 762
      removed outlier: 3.897A  pdb=" N   LYS A 762 " --> pdb=" O   THR A 759 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 759 through 762'
    Processing helix  chain 'A' and resid 763 through 771
    Processing helix  chain 'A' and resid 772 through 793
      removed outlier: 4.018A  pdb=" N   GLU A 783 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   LYS A 784 " --> pdb=" O   GLU A 780 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83
      removed outlier: 6.573A  pdb=" N   ALA A  73 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS A 424 " --> pdb=" O   GLN A 434 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLU A 432 " --> pdb=" O   GLN A 426 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 109
      removed outlier: 6.074A  pdb=" N   ILE A 108 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 180
      removed outlier: 7.352A  pdb=" N   ALA A 305 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   VAL A 340 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   VAL A 307 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   HIS A 342 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   VAL A 309 " --> pdb=" O   HIS A 342 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL A 417 " --> pdb=" O   HIS A 367 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL A 369 " --> pdb=" O   VAL A 417 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 186
      removed outlier: 3.650A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 286
    Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 604
      removed outlier: 6.980A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   VAL A 579 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL A 542 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   SER A 511 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL A 542 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   THR A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE A 506 " --> pdb=" O   THR A 510 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU A 503 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   PHE A 485 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ASN A 505 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   ILE A 483 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   MET A 750 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 634 through 641
      removed outlier: 4.914A  pdb=" N   VAL A 654 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   PHE A 637 " --> pdb=" O   ALA A 652 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ALA A 652 " --> pdb=" O   PHE A 637 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   THR A 639 " --> pdb=" O   GLY A 650 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   GLY A 650 " --> pdb=" O   THR A 639 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LYS A 660 " --> pdb=" O   LEU A 682 " (cutoff:3.500A)
      removed outlier: 8.679A  pdb=" N   ILE A 684 " --> pdb=" O   LYS A 660 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL A 662 " --> pdb=" O   ILE A 684 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU A 683 " --> pdb=" O   MET A 721 " (cutoff:3.500A)

    183 hydrogen bonds defined for protein.
    522 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      38 hydrogen bonds
      72 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 2.95

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6118
        1.03 -     1.23: 98
        1.23 -     1.43: 3087
        1.43 -     1.62: 3913
        1.62 -     1.82: 56
  Bond restraints: 13272
  Sorted by residual:
  bond pdb=" N   SER A  52 "
       pdb=" CA  SER A  52 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   SER A  52 "
       pdb=" H   SER A  52 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.35e+00
  bond pdb=" C   ILE A 183 "
       pdb=" O   ILE A 183 "
    ideal  model  delta    sigma   weight residual
    1.232  1.241 -0.009 1.01e-02 9.80e+03 8.30e-01
  bond pdb=" CA  THR A  57 "
       pdb=" CB  THR A  57 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.35e-02 5.49e+03 7.47e-01
  bond pdb=" C   MET A 760 "
       pdb=" N   PRO A 761 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.69e-01
  ... (remaining 13267 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.74: 23992
        6.74 -    13.47: 6
       13.47 -    20.21: 0
       20.21 -    26.94: 2
       26.94 -    33.68: 6
  Bond angle restraints: 24006
  Sorted by residual:
  angle pdb=" N9    A T  32 "
        pdb=" C1'   A T  32 "
        pdb=" H1'   A T  32 "
      ideal   model   delta    sigma   weight residual
     109.00   75.32   33.68 3.00e+00 1.11e-01 1.26e+02
  angle pdb=" N9    A T  66 "
        pdb=" C1'   A T  66 "
        pdb=" H1'   A T  66 "
      ideal   model   delta    sigma   weight residual
     109.00   75.65   33.35 3.00e+00 1.11e-01 1.24e+02
  angle pdb=" C2'   A T  32 "
        pdb=" C1'   A T  32 "
        pdb=" H1'   A T  32 "
      ideal   model   delta    sigma   weight residual
     109.00   79.78   29.22 3.00e+00 1.11e-01 9.49e+01
  angle pdb=" C2'   A T  66 "
        pdb=" C1'   A T  66 "
        pdb=" H1'   A T  66 "
      ideal   model   delta    sigma   weight residual
     109.00   79.84   29.16 3.00e+00 1.11e-01 9.45e+01
  angle pdb=" O4'   A T  66 "
        pdb=" C1'   A T  66 "
        pdb=" H1'   A T  66 "
      ideal   model   delta    sigma   weight residual
     109.00   80.38   28.62 3.00e+00 1.11e-01 9.10e+01
  ... (remaining 24001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.56: 5872
       28.56 -    57.11: 343
       57.11 -    85.67: 110
       85.67 -   114.23: 4
      114.23 -   142.78: 1
  Dihedral angle restraints: 6330
    sinusoidal: 4024
      harmonic: 2306
  Sorted by residual:
  dihedral pdb=" O4'   U T  60 "
           pdb=" C1'   U T  60 "
           pdb=" N1    U T  60 "
           pdb=" C2    U T  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -17.22 -142.78     1      1.50e+01 4.44e-03 7.66e+01
  dihedral pdb=" O4'   U T  37 "
           pdb=" C1'   U T  37 "
           pdb=" N1    U T  37 "
           pdb=" C2    U T  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   86.82  113.18     1      1.50e+01 4.44e-03 5.95e+01
  dihedral pdb=" O4'   C T  36 "
           pdb=" C1'   C T  36 "
           pdb=" N1    C T  36 "
           pdb=" C2    C T  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -76.44  -83.56     1      1.50e+01 4.44e-03 3.79e+01
  ... (remaining 6327 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.381: 1178
       0.381 -    0.762: 0
       0.762 -    1.142: 2
       1.142 -    1.523: 0
       1.523 -    1.904: 1
  Chirality restraints: 1181
  Sorted by residual:
  chirality pdb=" P     A T  66 "
            pdb=" OP1   A T  66 "
            pdb=" OP2   A T  66 "
            pdb=" O5'   A T  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.51    1.90 2.00e-01 2.50e+01 9.06e+01
  chirality pdb=" C1'   A T  66 "
            pdb=" O4'   A T  66 "
            pdb=" C2'   A T  66 "
            pdb=" N9    A T  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    1.58    0.88 2.00e-01 2.50e+01 1.95e+01
  chirality pdb=" C1'   A T  32 "
            pdb=" O4'   A T  32 "
            pdb=" C2'   A T  32 "
            pdb=" N9    A T  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    1.58    0.88 2.00e-01 2.50e+01 1.92e+01
  ... (remaining 1178 not shown)

  Planarity restraints: 1731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 623 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.71e+00
        pdb=" C   ARG A 623 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ARG A 623 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 624 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 251 "    0.160 9.50e-02 1.11e+02   5.35e-02 3.13e+00
        pdb=" NE  ARG A 251 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 251 "    0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 251 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 251 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A 251 "   -0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG A 251 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 251 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 251 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 764 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.72e+00
        pdb=" N   PRO A 765 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 765 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 765 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1728 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 400
        2.15 -     2.76: 22519
        2.76 -     3.37: 34606
        3.37 -     3.99: 43210
        3.99 -     4.60: 67486
  Nonbonded interactions: 168221
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 591 "
            pdb=" HD1 HIS A 592 "
     model   vdw
     1.534 2.450
  nonbonded pdb=" O6    G T   9 "
            pdb=" H62   A T  19 "
     model   vdw
     1.643 2.450
  nonbonded pdb="HD21 ASN A 390 "
            pdb=" O   PHE A 397 "
     model   vdw
     1.646 2.450
  nonbonded pdb=" H   ILE A 720 "
            pdb=" O   LYS A 742 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" OE1 GLU A 145 "
            pdb=" H   GLU A 145 "
     model   vdw
     1.656 2.450
  ... (remaining 168216 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:             5.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.040
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     18.170
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
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      :  0.002   0.033   7139  Z= 0.101
  Angle     :  0.662  26.347   9999  Z= 0.324
  Chirality :  0.075   1.904   1181
  Planarity :  0.004   0.070   1037
  Dihedral  : 19.188 142.782   3101
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.96 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 18.24 %
    Favored  : 80.74 %
  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:  1.26 (0.35), residues: 682
  helix:  2.27 (0.39), residues: 210
  sheet:  0.93 (0.53), residues: 128
  loop : -0.07 (0.36), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 251 
 TYR   0.005   0.000   TYR A 528 
 PHE   0.006   0.000   PHE A 521 
 TRP   0.002   0.000   TRP A 115 
 HIS   0.003   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 7134)
  covalent geometry    : angle       0.66179 ( 9999)
  hydrogen bonds       : bond        0.19747 (  221)
  hydrogen bonds       : angle       6.66651 (  594)
  metal coordination   : bond        0.00038 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7361 (mmm) cc_final: 0.7097 (tpt)
REVERT: A  264 LEU cc_start: 0.5044 (OUTLIER) cc_final: 0.4667 (mt)
REVERT: A  289 ARG cc_start: 0.7506 (ptm160) cc_final: 0.7281 (ptm160)
REVERT: A  358 MET cc_start: 0.7516 (ptt) cc_final: 0.7234 (ptt)
REVERT: A  604 MET cc_start: 0.7297 (ptt) cc_final: 0.6972 (ptm)
  outliers start: 6
  outliers final: 3
  residues processed: 81
  average time/residue: 0.2056
  time to fit residues: 22.0435
Evaluate side-chains
  75 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  775 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 330 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.198549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.152110 restraints weight = 31808.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.159722 restraints weight = 15678.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.164479 restraints weight = 10229.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.167553 restraints weight = 7769.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.169286 restraints weight = 6423.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7139  Z= 0.162
  Angle     :  0.707  26.812   9999  Z= 0.343
  Chirality :  0.076   1.883   1181
  Planarity :  0.005   0.051   1037
  Dihedral  : 18.759 141.248   1789
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.87 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.55 %
    Favored  : 80.57 %
  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:  0.86 (0.35), residues: 682
  helix:  1.96 (0.37), residues: 211
  sheet:  0.44 (0.52), residues: 126
  loop : -0.20 (0.36), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 251 
 TYR   0.008   0.001   TYR A 663 
 PHE   0.017   0.001   PHE A  85 
 TRP   0.008   0.002   TRP A 115 
 HIS   0.004   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7134)
  covalent geometry    : angle       0.70745 ( 9999)
  hydrogen bonds       : bond        0.05235 (  221)
  hydrogen bonds       : angle       4.92621 (  594)
  metal coordination   : bond        0.00499 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7500 (mmm) cc_final: 0.7228 (tpt)
REVERT: A  264 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4451 (mp)
REVERT: A  289 ARG cc_start: 0.7647 (ptm160) cc_final: 0.7423 (ptm160)
REVERT: A  358 MET cc_start: 0.7673 (ptt) cc_final: 0.7413 (ptt)
REVERT: A  604 MET cc_start: 0.7307 (ptt) cc_final: 0.6951 (ptm)
  outliers start: 17
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1597
  time to fit residues: 18.8462
Evaluate side-chains
  89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  442 ASN
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  651 CYS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  716 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 738 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.198465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.151489 restraints weight = 31400.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.159209 restraints weight = 15182.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.163945 restraints weight = 9855.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.166986 restraints weight = 7479.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.168904 restraints weight = 6202.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6784
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7139  Z= 0.102
  Angle     :  0.655  26.630   9999  Z= 0.310
  Chirality :  0.075   1.906   1181
  Planarity :  0.004   0.041   1037
  Dihedral  : 18.729 140.642   1785
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.99 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.57 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.35), residues: 682
  helix:  2.09 (0.38), residues: 212
  sheet:  0.33 (0.51), residues: 126
  loop : -0.14 (0.37), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 497 
 TYR   0.006   0.001   TYR A 147 
 PHE   0.008   0.001   PHE A 109 
 TRP   0.009   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 7134)
  covalent geometry    : angle       0.65496 ( 9999)
  hydrogen bonds       : bond        0.04319 (  221)
  hydrogen bonds       : angle       4.62116 (  594)
  metal coordination   : bond        0.00138 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7499 (mmm) cc_final: 0.7208 (tpt)
REVERT: A  264 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4411 (mp)
REVERT: A  289 ARG cc_start: 0.7676 (ptm160) cc_final: 0.7425 (ptm160)
REVERT: A  358 MET cc_start: 0.7706 (ptt) cc_final: 0.7488 (ptt)
REVERT: A  604 MET cc_start: 0.7349 (ptt) cc_final: 0.6974 (ptm)
  outliers start: 17
  outliers final: 12
  residues processed: 83
  average time/residue: 0.2006
  time to fit residues: 22.4793
Evaluate side-chains
  91 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  716 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.196372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.153055 restraints weight = 31899.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.160052 restraints weight = 15739.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.164368 restraints weight = 10385.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.167055 restraints weight = 7928.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.168586 restraints weight = 6660.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7139  Z= 0.162
  Angle     :  0.707  26.707   9999  Z= 0.345
  Chirality :  0.076   1.913   1181
  Planarity :  0.004   0.043   1037
  Dihedral  : 18.922 135.872   1785
  Min Nonbonded Distance : 1.763

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.45 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.23 %
    Favored  : 79.39 %
  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:  0.59 (0.35), residues: 682
  helix:  1.90 (0.37), residues: 213
  sheet: -0.24 (0.49), residues: 126
  loop : -0.27 (0.36), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 251 
 TYR   0.009   0.001   TYR A 663 
 PHE   0.015   0.002   PHE A  85 
 TRP   0.009   0.002   TRP A 115 
 HIS   0.007   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 7134)
  covalent geometry    : angle       0.70668 ( 9999)
  hydrogen bonds       : bond        0.04199 (  221)
  hydrogen bonds       : angle       4.41679 (  594)
  metal coordination   : bond        0.00403 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 ASP cc_start: 0.7870 (t0) cc_final: 0.7621 (t0)
REVERT: A  604 MET cc_start: 0.7381 (ptt) cc_final: 0.7020 (ptm)
  outliers start: 20
  outliers final: 17
  residues processed: 88
  average time/residue: 0.1748
  time to fit residues: 21.0359
Evaluate side-chains
  91 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  442 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  738 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 43 optimal weight:    0.2980
   chunk 37 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 46 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4575 r_free = 0.4575 target = 0.197638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.154693 restraints weight = 31821.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.161739 restraints weight = 15464.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.166115 restraints weight = 10127.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.168819 restraints weight = 7721.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.170322 restraints weight = 6441.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7139  Z= 0.099
  Angle     :  0.660  26.592   9999  Z= 0.314
  Chirality :  0.076   1.928   1181
  Planarity :  0.004   0.044   1037
  Dihedral  : 18.830 133.860   1779
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.72 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.40 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.35), residues: 682
  helix:  2.14 (0.38), residues: 213
  sheet: -0.34 (0.49), residues: 126
  loop : -0.19 (0.37), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 782 
 TYR   0.006   0.001   TYR A 463 
 PHE   0.008   0.001   PHE A 521 
 TRP   0.010   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 7134)
  covalent geometry    : angle       0.66001 ( 9999)
  hydrogen bonds       : bond        0.03550 (  221)
  hydrogen bonds       : angle       4.26833 (  594)
  metal coordination   : bond        0.00169 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 ASP cc_start: 0.7858 (t0) cc_final: 0.7616 (t0)
REVERT: A  604 MET cc_start: 0.7411 (ptt) cc_final: 0.7023 (ptm)
  outliers start: 17
  outliers final: 17
  residues processed: 84
  average time/residue: 0.1745
  time to fit residues: 20.2405
Evaluate side-chains
  90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  716 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 38 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    1.3364

-------------------------------------------------------------------------------
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 = 0.4557 r_free = 0.4557 target = 0.196051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.152611 restraints weight = 31563.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.159597 restraints weight = 15769.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.163901 restraints weight = 10438.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.166287 restraints weight = 8011.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.168227 restraints weight = 6819.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7139  Z= 0.122
  Angle     :  0.663  26.552   9999  Z= 0.317
  Chirality :  0.076   1.924   1181
  Planarity :  0.004   0.044   1037
  Dihedral  : 18.863 130.901   1779
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.89 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.74 %
    Favored  : 78.89 %
  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:  0.72 (0.35), residues: 682
  helix:  2.16 (0.38), residues: 213
  sheet: -0.43 (0.49), residues: 126
  loop : -0.19 (0.37), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 251 
 TYR   0.007   0.001   TYR A 663 
 PHE   0.010   0.001   PHE A 109 
 TRP   0.010   0.002   TRP A 115 
 HIS   0.005   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7134)
  covalent geometry    : angle       0.66319 ( 9999)
  hydrogen bonds       : bond        0.03445 (  221)
  hydrogen bonds       : angle       4.23963 (  594)
  metal coordination   : bond        0.00295 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.6432 (mm-30) cc_final: 0.5890 (pp20)
REVERT: A  301 ASP cc_start: 0.7825 (t0) cc_final: 0.7618 (t0)
REVERT: A  358 MET cc_start: 0.8082 (ptm) cc_final: 0.7624 (ptt)
REVERT: A  417 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7265 (m)
REVERT: A  604 MET cc_start: 0.7394 (ptt) cc_final: 0.6999 (ptm)
  outliers start: 20
  outliers final: 16
  residues processed: 86
  average time/residue: 0.1654
  time to fit residues: 19.7878
Evaluate side-chains
  92 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  442 ASN
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  775 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 373 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.193367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.149744 restraints weight = 31606.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.156588 restraints weight = 15915.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.160907 restraints weight = 10610.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.163233 restraints weight = 8192.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.165104 restraints weight = 7000.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7139  Z= 0.153
  Angle     :  0.697  26.433   9999  Z= 0.339
  Chirality :  0.077   1.941   1181
  Planarity :  0.004   0.045   1037
  Dihedral  : 18.972 125.944   1779
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.04 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 17.57 %
    Favored  : 78.55 %
  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:  0.41 (0.35), residues: 682
  helix:  1.90 (0.37), residues: 215
  sheet: -0.80 (0.48), residues: 131
  loop : -0.28 (0.38), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 104 
 TYR   0.008   0.001   TYR A 663 
 PHE   0.013   0.002   PHE A 109 
 TRP   0.007   0.002   TRP A 115 
 HIS   0.006   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7134)
  covalent geometry    : angle       0.69728 ( 9999)
  hydrogen bonds       : bond        0.03712 (  221)
  hydrogen bonds       : angle       4.29665 (  594)
  metal coordination   : bond        0.00439 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.6465 (mm-30) cc_final: 0.5918 (pp20)
REVERT: A  301 ASP cc_start: 0.7859 (t0) cc_final: 0.7646 (t0)
REVERT: A  358 MET cc_start: 0.8255 (ptm) cc_final: 0.7712 (ptt)
  outliers start: 23
  outliers final: 19
  residues processed: 88
  average time/residue: 0.1429
  time to fit residues: 17.9535
Evaluate side-chains
  93 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLN
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  442 ASN
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  568 SER
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  738 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    0.0970
   chunk 34 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   overall best weight:    1.4982

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

Flipped N/Q/H residues before XYZ refinement:
A 644 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.193647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.148963 restraints weight = 31687.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.155998 restraints weight = 16012.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.160284 restraints weight = 10710.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.162966 restraints weight = 8318.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.164484 restraints weight = 7025.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7139  Z= 0.131
  Angle     :  0.688  26.393   9999  Z= 0.334
  Chirality :  0.077   1.943   1181
  Planarity :  0.004   0.045   1037
  Dihedral  : 18.942 125.824   1779
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.33 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.41 %
    Favored  : 78.21 %
  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:  0.40 (0.35), residues: 682
  helix:  1.89 (0.37), residues: 215
  sheet: -0.89 (0.47), residues: 131
  loop : -0.24 (0.38), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 782 
 TYR   0.007   0.001   TYR A 463 
 PHE   0.010   0.001   PHE A 109 
 TRP   0.010   0.001   TRP A 115 
 HIS   0.006   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7134)
  covalent geometry    : angle       0.68786 ( 9999)
  hydrogen bonds       : bond        0.03603 (  221)
  hydrogen bonds       : angle       4.26491 (  594)
  metal coordination   : bond        0.00358 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.6438 (mm-30) cc_final: 0.5899 (pp20)
REVERT: A  301 ASP cc_start: 0.7867 (t0) cc_final: 0.7658 (t0)
REVERT: A  358 MET cc_start: 0.8260 (ptm) cc_final: 0.7741 (ptt)
  outliers start: 20
  outliers final: 17
  residues processed: 87
  average time/residue: 0.1423
  time to fit residues: 17.7506
Evaluate side-chains
  90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  442 ASN
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  568 SER
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  716 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.4531 r_free = 0.4531 target = 0.193529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.148959 restraints weight = 31820.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.156080 restraints weight = 15969.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.160313 restraints weight = 10623.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.163027 restraints weight = 8247.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.164752 restraints weight = 6955.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7139  Z= 0.124
  Angle     :  0.681  26.353   9999  Z= 0.327
  Chirality :  0.077   1.945   1181
  Planarity :  0.004   0.046   1037
  Dihedral  : 18.912 125.408   1779
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.33 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.09 %
    Favored  : 77.87 %
  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:  0.38 (0.35), residues: 682
  helix:  1.95 (0.37), residues: 215
  sheet: -1.03 (0.46), residues: 132
  loop : -0.26 (0.38), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 782 
 TYR   0.007   0.001   TYR A 463 
 PHE   0.009   0.001   PHE A 109 
 TRP   0.009   0.002   TRP A 115 
 HIS   0.005   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7134)
  covalent geometry    : angle       0.68071 ( 9999)
  hydrogen bonds       : bond        0.03454 (  221)
  hydrogen bonds       : angle       4.23843 (  594)
  metal coordination   : bond        0.00389 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.6427 (mm-30) cc_final: 0.5897 (pp20)
REVERT: A  358 MET cc_start: 0.8273 (ptm) cc_final: 0.7766 (ptt)
REVERT: A  417 VAL cc_start: 0.7583 (OUTLIER) cc_final: 0.7336 (m)
  outliers start: 18
  outliers final: 15
  residues processed: 84
  average time/residue: 0.1445
  time to fit residues: 17.4893
Evaluate side-chains
  87 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  442 ASN
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  568 SER
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  716 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 531 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.191781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.147178 restraints weight = 31883.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.154130 restraints weight = 15903.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.158550 restraints weight = 10536.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.161234 restraints weight = 8111.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.162692 restraints weight = 6836.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7139  Z= 0.149
  Angle     :  0.698  26.285   9999  Z= 0.339
  Chirality :  0.077   1.948   1181
  Planarity :  0.004   0.046   1037
  Dihedral  : 18.932 124.426   1779
  Min Nonbonded Distance : 1.769

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.36 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.26 %
    Favored  : 77.70 %
  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:  0.19 (0.35), residues: 682
  helix:  1.88 (0.37), residues: 215
  sheet: -1.12 (0.46), residues: 132
  loop : -0.44 (0.38), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 104 
 TYR   0.008   0.001   TYR A 663 
 PHE   0.011   0.001   PHE A 109 
 TRP   0.007   0.002   TRP A 115 
 HIS   0.006   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7134)
  covalent geometry    : angle       0.69827 ( 9999)
  hydrogen bonds       : bond        0.03577 (  221)
  hydrogen bonds       : angle       4.33638 (  594)
  metal coordination   : bond        0.00536 (    5)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.6451 (mm-30) cc_final: 0.5905 (pp20)
REVERT: A  358 MET cc_start: 0.8282 (ptm) cc_final: 0.7794 (ptt)
REVERT: A  417 VAL cc_start: 0.7591 (OUTLIER) cc_final: 0.7340 (m)
  outliers start: 18
  outliers final: 16
  residues processed: 80
  average time/residue: 0.1498
  time to fit residues: 17.0226
Evaluate side-chains
  87 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  428 ARG
Chi-restraints excluded: chain A residue  442 ASN
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  568 SER
Chi-restraints excluded: chain A residue  574 HIS
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  716 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 531 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.191709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.147772 restraints weight = 31778.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.154619 restraints weight = 15938.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.159015 restraints weight = 10705.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.161727 restraints weight = 8244.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.163263 restraints weight = 6924.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7139  Z= 0.146
  Angle     :  0.696  26.152   9999  Z= 0.339
  Chirality :  0.077   1.957   1181
  Planarity :  0.004   0.046   1037
  Dihedral  : 18.949 123.776   1779
  Min Nonbonded Distance : 1.784

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.77 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.75 %
    Favored  : 77.87 %
  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:  0.15 (0.35), residues: 682
  helix:  1.83 (0.37), residues: 215
  sheet: -1.15 (0.47), residues: 130
  loop : -0.45 (0.38), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 104 
 TYR   0.008   0.001   TYR A 463 
 PHE   0.011   0.001   PHE A 109 
 TRP   0.005   0.002   TRP A 115 
 HIS   0.006   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7134)
  covalent geometry    : angle       0.69614 ( 9999)
  hydrogen bonds       : bond        0.03576 (  221)
  hydrogen bonds       : angle       4.33907 (  594)
  metal coordination   : bond        0.00434 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2906.52 seconds
wall clock time: 50 minutes 8.54 seconds (3008.54 seconds total)