Starting phenix.real_space_refine
on Thu Jul  2 03:09:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ca4_45380/07_2026/9ca4_45380_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ca4_45380/07_2026/9ca4_45380.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ca4_45380/07_2026/9ca4_45380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ca4_45380/07_2026/9ca4_45380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ca4_45380/07_2026/9ca4_45380_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ca4_45380/07_2026/9ca4_45380_neut.cif"
  }
  resolution = 3.01
  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=   0.001 sd=   0.020
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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       8      5.49       5
     S      39      5.16       5
     C    3905      2.51       5
     N    1076      2.21       5
     O    1200      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6230
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4843
          Classifications: {'peptide': 612}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 581}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'PTR:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 1219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1219
          Classifications: {'peptide': 161}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 153}
    Chain: "E"
      Number of atoms: 128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 128
          Classifications: {'RNA': 6}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
    Chain: "G"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Classifications: {'RNA': 2}
          Modifications used: {'5*END': 1, 'rna2p_pyr': 1}
          Link IDs: {'rna3p': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 0
          Ad-hoc single atom residues: {' MN': 2}
          Chain breaks: 2
  Time building chain proxies: 1.48, per 1000 atoms: 0.24
  Number of scatterers: 6230
  At special positions: 0
  Unit cell: (73.87, 87.98, 135.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      39     16.00
     P       8     15.00
     O    1200      8.00
     N    1076      7.00
     C    3905      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 332.1 milliseconds
  

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1442

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 5 sheets defined
      42.6% alpha, 16.7% beta
      0 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 20
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 3.858A  pdb=" N   PHE A  82 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 106
    Processing helix  chain 'A' and resid 119 through 134
    Processing helix  chain 'A' and resid 156 through 166
    Processing helix  chain 'A' and resid 171 through 204
      removed outlier: 4.253A  pdb=" N   ALA A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   GLY A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   PHE A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLY A 202 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 208
    Processing helix  chain 'A' and resid 218 through 234
      removed outlier: 3.620A  pdb=" N   CYS A 225 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 276
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 317 through 332
    Processing helix  chain 'A' and resid 349 through 356
    Processing helix  chain 'A' and resid 357 through 360
      removed outlier: 3.602A  pdb=" N   HIS A 360 " --> pdb=" O   GLN A 357 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 357 through 360'
    Processing helix  chain 'A' and resid 363 through 373
      removed outlier: 3.565A  pdb=" N   ALA A 372 " --> pdb=" O   LYS A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 402
      removed outlier: 3.561A  pdb=" N   LEU A 401 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.746A  pdb=" N   ARG A 407 " --> pdb=" O   GLY A 403 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 408 " --> pdb=" O   ASP A 404 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 417 " --> pdb=" O   THR A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 454
      removed outlier: 3.743A  pdb=" N   GLU A 454 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 506
      removed outlier: 3.727A  pdb=" N   THR A 501 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 524
      removed outlier: 4.221A  pdb=" N   VAL A 516 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 552
      removed outlier: 3.756A  pdb=" N   VAL A 543 " --> pdb=" O   ASN A 539 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS A 550 " --> pdb=" O   HIS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 557
      removed outlier: 4.570A  pdb=" N   LEU A 557 " --> pdb=" O   GLU A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 573
      removed outlier: 4.198A  pdb=" N   SER A 562 " --> pdb=" O   PRO A 558 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 571 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 599
      removed outlier: 3.737A  pdb=" N   LYS A 592 " --> pdb=" O   VAL A 588 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER A 599 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 611
      removed outlier: 3.873A  pdb=" N   ASP A 604 " --> pdb=" O   ILE A 600 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU A 605 " --> pdb=" O   ALA A 601 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LEU A 606 " --> pdb=" O   GLY A 602 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   VAL A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER A 610 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 19 through 25
      removed outlier: 3.577A  pdb=" N   THR B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 43
      removed outlier: 4.530A  pdb=" N   LEU B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE B  39 " --> pdb=" O   ASP B  35 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B  40 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ASN B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 147
      removed outlier: 3.553A  pdb=" N   ASN B 146 " --> pdb=" O   ASN B 143 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR B 147 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 143 through 147'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29
      removed outlier: 6.627A  pdb=" N   LYS A   2 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   VAL A   4 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   THR A  55 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   MET A   6 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   THR A   3 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   VAL A 113 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU A   5 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE A 112 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66
    Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 449
      removed outlier: 6.904A  pdb=" N   LYS A 425 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A 245 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   TRP A 259 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   LEU A 243 " --> pdb=" O   TRP A 259 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 480 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ASN A 248 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   VAL A 478 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE A 476 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL A 285 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ARG A 434 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA A 287 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR A 430 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 530
    Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65
      removed outlier: 4.499A  pdb=" N   ASP B 134 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 9.337A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   THR B 107 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   LEU B 142 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   LYS B 126 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)

    250 hydrogen bonds defined for protein.
    705 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      4 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1728
        1.33 -     1.45: 1037
        1.45 -     1.57: 3531
        1.57 -     1.69: 13
        1.69 -     1.81: 62
  Bond restraints: 6371
  Sorted by residual:
  bond pdb=" OH  PTR A 336 "
       pdb=" P   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.769  1.608  0.161 2.00e-02 2.50e+03 6.48e+01
  bond pdb=" C   SER A 335 "
       pdb=" N   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.23e+01
  bond pdb=" N   GLU A 465 "
       pdb=" CA  GLU A 465 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.57e+00
  bond pdb=" O3'   U E  -1 "
       pdb=" P     A E   0 "
    ideal  model  delta    sigma   weight residual
    1.607  1.567  0.040 1.50e-02 4.44e+03 6.98e+00
  bond pdb=" N   ASN A  71 "
       pdb=" CA  ASN A  71 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.70e+00
  ... (remaining 6366 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.59: 8650
        7.59 -    15.18: 4
       15.18 -    22.77: 1
       22.77 -    30.36: 0
       30.36 -    37.96: 2
  Bond angle restraints: 8657
  Sorted by residual:
  angle pdb=" O   SER A 335 "
        pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
      ideal   model   delta    sigma   weight residual
     123.00   85.04   37.96 1.60e+00 3.91e-01 5.63e+02
  angle pdb=" CA  SER A 335 "
        pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
      ideal   model   delta    sigma   weight residual
     116.20  149.47  -33.27 2.00e+00 2.50e-01 2.77e+02
  angle pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
        pdb=" CA  PTR A 336 "
      ideal   model   delta    sigma   weight residual
     121.70  138.72  -17.02 1.80e+00 3.09e-01 8.94e+01
  angle pdb=" C   GLU A 465 "
        pdb=" N   SER A 466 "
        pdb=" CA  SER A 466 "
      ideal   model   delta    sigma   weight residual
     122.95  114.97    7.98 1.44e+00 4.82e-01 3.07e+01
  angle pdb=" C   ASN A  71 "
        pdb=" CA  ASN A  71 "
        pdb=" CB  ASN A  71 "
      ideal   model   delta    sigma   weight residual
     110.42  101.56    8.86 1.99e+00 2.53e-01 1.98e+01
  ... (remaining 8652 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 3423
       17.54 -    35.08: 344
       35.08 -    52.61: 79
       52.61 -    70.15: 15
       70.15 -    87.69: 5
  Dihedral angle restraints: 3866
    sinusoidal: 1632
      harmonic: 2234
  Sorted by residual:
  dihedral pdb=" CA  SER A 335 "
           pdb=" C   SER A 335 "
           pdb=" N   PTR A 336 "
           pdb=" CA  PTR A 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.64  -28.36     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" O4'   A E   0 "
           pdb=" C2'   A E   0 "
           pdb=" C1'   A E   0 "
           pdb=" C3'   A E   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -1.81   26.81     1      8.00e+00 1.56e-02 1.61e+01
  dihedral pdb=" C4'   A E   0 "
           pdb=" O4'   A E   0 "
           pdb=" C1'   A E   0 "
           pdb=" C2'   A E   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -22.17   25.17     1      8.00e+00 1.56e-02 1.42e+01
  ... (remaining 3863 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 730
       0.044 -    0.088: 179
       0.088 -    0.131: 55
       0.131 -    0.175: 11
       0.175 -    0.219: 2
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" C3'   A E   0 "
            pdb=" C4'   A E   0 "
            pdb=" O3'   A E   0 "
            pdb=" C2'   A E   0 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.70    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  LEU A 134 "
            pdb=" N   LEU A 134 "
            pdb=" C   LEU A 134 "
            pdb=" CB  LEU A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.75e-01
  chirality pdb=" C3'   A E   1 "
            pdb=" C4'   A E   1 "
            pdb=" O3'   A E   1 "
            pdb=" C2'   A E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.65    0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 974 not shown)

  Planarity restraints: 1090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 335 "    0.048 2.00e-02 2.50e+03   6.95e-02 4.83e+01
        pdb=" C   SER A 335 "   -0.120 2.00e-02 2.50e+03
        pdb=" O   SER A 335 "    0.028 2.00e-02 2.50e+03
        pdb=" N   PTR A 336 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 456 "    0.051 5.00e-02 4.00e+02   7.68e-02 9.43e+00
        pdb=" N   PRO A 457 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 457 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 457 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 464 "   -0.015 2.00e-02 2.50e+03   2.83e-02 7.99e+00
        pdb=" C   GLU A 464 "    0.049 2.00e-02 2.50e+03
        pdb=" O   GLU A 464 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLU A 465 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1087 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 85
        2.65 -     3.21: 5606
        3.21 -     3.78: 8814
        3.78 -     4.34: 11790
        4.34 -     4.90: 19739
  Nonbonded interactions: 46034
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   9 "
            pdb="MN    MN A 702 "
     model   vdw
     2.091 3.060
  nonbonded pdb=" OE2 GLU A 340 "
            pdb=" OD2 ASP A 511 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OD2 ASP A 117 "
            pdb="MN    MN A 702 "
     model   vdw
     2.164 3.060
  nonbonded pdb=" OD2 ASP A 511 "
            pdb="MN    MN A 701 "
     model   vdw
     2.168 3.060
  nonbonded pdb=" O   ASP A 185 "
            pdb=" O2'   U E  -1 "
     model   vdw
     2.199 3.040
  ... (remaining 46029 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.410
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.820
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
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      :  0.005   0.203   6372  Z= 0.348
  Angle     :  0.871  37.956   8657  Z= 0.484
  Chirality :  0.045   0.219    977
  Planarity :  0.006   0.077   1090
  Dihedral  : 14.819  87.692   2424
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.14 %
  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 (0.30), residues: 766
  helix:  0.35 (0.30), residues: 291
  sheet:  0.26 (0.48), residues: 137
  loop : -0.93 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 434 
 TYR   0.016   0.002   TYR A 240 
 PHE   0.018   0.002   PHE A 265 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00465 /  0.24 ( 6371)
  covalent geometry    : angle       0.87100 /  0.48 ( 8657)
  hydrogen bonds       : bond        0.19650 / 13.25 (  250)
  hydrogen bonds       : angle       5.89950 /  4.04 (  705)
  Misc. bond           : bond        0.20258 / 10.66 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ASN cc_start: 0.7593 (t0) cc_final: 0.7389 (t0)
REVERT: A  185 ASP cc_start: 0.7302 (m-30) cc_final: 0.7096 (m-30)
REVERT: A  285 VAL cc_start: 0.8386 (p) cc_final: 0.8097 (m)
REVERT: A  431 ILE cc_start: 0.8354 (mm) cc_final: 0.8135 (mt)
REVERT: A  505 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8304 (ttpp)
REVERT: A  528 THR cc_start: 0.7886 (p) cc_final: 0.7466 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0602
  time to fit residues: 17.4374
Evaluate side-chains
  203 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0050
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 74 optimal weight:    0.0470
   overall best weight:    0.3092

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.124315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.110389 restraints weight = 10237.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.62
r_work: 0.3402 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6372  Z= 0.141
  Angle     :  0.622  11.144   8657  Z= 0.320
  Chirality :  0.043   0.204    977
  Planarity :  0.005   0.060   1090
  Dihedral  :  8.472  73.405    940
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 14.11 %
    Favored  : 84.83 %
  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: -0.13 (0.30), residues: 766
  helix:  0.68 (0.30), residues: 292
  sheet:  0.42 (0.49), residues: 128
  loop : -0.90 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 434 
 TYR   0.016   0.002   TYR A 426 
 PHE   0.030   0.002   PHE A 214 
 TRP   0.009   0.001   TRP A 406 
 HIS   0.002   0.000   HIS A 584 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 ( 6371)
  covalent geometry    : angle       0.62182 /  0.32 ( 8657)
  hydrogen bonds       : bond        0.05609 /  3.79 (  250)
  hydrogen bonds       : angle       4.78532 /  3.25 (  705)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 199
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ASN cc_start: 0.8037 (t0) cc_final: 0.7741 (t0)
REVERT: A  124 ASN cc_start: 0.8220 (t0) cc_final: 0.7963 (t0)
REVERT: A  185 ASP cc_start: 0.7704 (m-30) cc_final: 0.7469 (m-30)
REVERT: A  232 ILE cc_start: 0.8583 (mm) cc_final: 0.8291 (tp)
REVERT: A  234 SER cc_start: 0.8778 (t) cc_final: 0.8515 (p)
REVERT: A  306 MET cc_start: 0.8110 (ttp) cc_final: 0.7862 (ttp)
REVERT: A  431 ILE cc_start: 0.8365 (mm) cc_final: 0.8143 (mt)
REVERT: A  465 GLU cc_start: 0.8106 (tp30) cc_final: 0.7338 (tt0)
REVERT: A  579 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7694 (mmm-85)
  outliers start: 7
  outliers final: 5
  residues processed: 200
  average time/residue: 0.0538
  time to fit residues: 14.8257
Evaluate side-chains
  201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 196
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  428 GLN
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain B residue  119 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 72 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0770
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0050
   chunk 21 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0570
   chunk 76 optimal weight:    0.3980
   overall best weight:    0.2070

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  71 ASN
A 347 ASN
A 428 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.124875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.110846 restraints weight = 10122.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.65
r_work: 0.3419 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6372  Z= 0.116
  Angle     :  0.562   9.797   8657  Z= 0.291
  Chirality :  0.041   0.181    977
  Planarity :  0.005   0.059   1090
  Dihedral  :  8.267  73.494    940
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.32 %
    Favored  : 83.33 %
  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:  0.02 (0.30), residues: 766
  helix:  0.85 (0.31), residues: 292
  sheet:  0.48 (0.48), residues: 128
  loop : -0.86 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 151 
 TYR   0.011   0.001   TYR A 240 
 PHE   0.025   0.001   PHE A 235 
 TRP   0.016   0.001   TRP A 241 
 HIS   0.001   0.000   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 ( 6371)
  covalent geometry    : angle       0.56202 /  0.29 ( 8657)
  hydrogen bonds       : bond        0.04880 /  3.30 (  250)
  hydrogen bonds       : angle       4.54167 /  3.07 (  705)
  Misc. bond           : bond        0.00085 /  0.04 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 183
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 ASP cc_start: 0.7813 (m-30) cc_final: 0.7499 (t0)
REVERT: A  164 MET cc_start: 0.8457 (tpp) cc_final: 0.7652 (tpp)
REVERT: A  185 ASP cc_start: 0.7729 (m-30) cc_final: 0.7442 (m-30)
REVERT: A  234 SER cc_start: 0.8745 (t) cc_final: 0.8430 (p)
REVERT: A  284 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7091 (mm-40)
REVERT: A  404 ASP cc_start: 0.8037 (m-30) cc_final: 0.7767 (t0)
REVERT: A  431 ILE cc_start: 0.8349 (mm) cc_final: 0.8129 (mt)
REVERT: A  526 TYR cc_start: 0.8581 (m-10) cc_final: 0.8157 (m-10)
REVERT: A  530 GLU cc_start: 0.6869 (pm20) cc_final: 0.6554 (pm20)
REVERT: A  569 ASN cc_start: 0.8796 (t0) cc_final: 0.8510 (t0)
REVERT: A  579 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7504 (mmm-85)
  outliers start: 9
  outliers final: 6
  residues processed: 184
  average time/residue: 0.0730
  time to fit residues: 18.1830
Evaluate side-chains
  183 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 177
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  71 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.122154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.108264 restraints weight = 10208.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.61
r_work: 0.3373 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6372  Z= 0.204
  Angle     :  0.572   9.668   8657  Z= 0.299
  Chirality :  0.044   0.186    977
  Planarity :  0.005   0.065   1090
  Dihedral  :  8.117  73.146    940
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.52 %
    Favored  : 81.23 %
  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: -0.04 (0.30), residues: 766
  helix:  0.77 (0.31), residues: 294
  sheet:  0.30 (0.48), residues: 132
  loop : -0.82 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 151 
 TYR   0.017   0.002   TYR A 426 
 PHE   0.024   0.002   PHE A 235 
 TRP   0.009   0.001   TRP A 241 
 HIS   0.003   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00468 /  0.20 ( 6371)
  covalent geometry    : angle       0.57198 /  0.30 ( 8657)
  hydrogen bonds       : bond        0.05257 /  3.61 (  250)
  hydrogen bonds       : angle       4.56472 /  3.09 (  705)
  Misc. bond           : bond        0.00007 /  0.00 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 198
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.8248 (t0) cc_final: 0.8017 (t0)
REVERT: A  159 ASP cc_start: 0.7893 (m-30) cc_final: 0.7561 (t0)
REVERT: A  185 ASP cc_start: 0.7776 (m-30) cc_final: 0.7471 (m-30)
REVERT: A  234 SER cc_start: 0.8756 (t) cc_final: 0.8423 (p)
REVERT: A  282 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7410 (tm-30)
REVERT: A  404 ASP cc_start: 0.8065 (m-30) cc_final: 0.7797 (t0)
REVERT: A  431 ILE cc_start: 0.8392 (mm) cc_final: 0.8185 (mt)
REVERT: A  503 MET cc_start: 0.8212 (mtp) cc_final: 0.7972 (mtm)
REVERT: A  530 GLU cc_start: 0.7099 (pm20) cc_final: 0.6763 (pm20)
REVERT: A  552 ASP cc_start: 0.7759 (t0) cc_final: 0.7498 (t0)
REVERT: A  569 ASN cc_start: 0.8785 (t0) cc_final: 0.8457 (t0)
REVERT: A  579 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7507 (mmm-85)
  outliers start: 15
  outliers final: 13
  residues processed: 199
  average time/residue: 0.0777
  time to fit residues: 20.8980
Evaluate side-chains
  206 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 192
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   71 ASN
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 63 optimal weight:    0.0010
   chunk 11 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 50 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   overall best weight:    0.3586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.123163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.109308 restraints weight = 10345.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.64
r_work: 0.3387 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6372  Z= 0.123
  Angle     :  0.548  11.210   8657  Z= 0.281
  Chirality :  0.041   0.160    977
  Planarity :  0.005   0.064   1090
  Dihedral  :  8.046  73.250    940
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.27 %
    Favored  : 80.18 %
  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:  0.02 (0.30), residues: 766
  helix:  0.85 (0.31), residues: 292
  sheet:  0.35 (0.47), residues: 134
  loop : -0.81 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 151 
 TYR   0.015   0.001   TYR A 240 
 PHE   0.028   0.002   PHE A 214 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 6371)
  covalent geometry    : angle       0.54810 /  0.28 ( 8657)
  hydrogen bonds       : bond        0.04612 /  3.15 (  250)
  hydrogen bonds       : angle       4.40413 /  2.97 (  705)
  Misc. bond           : bond        0.00002 /  0.00 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.8244 (t0) cc_final: 0.8006 (t0)
REVERT: A  159 ASP cc_start: 0.7868 (m-30) cc_final: 0.7541 (t0)
REVERT: A  185 ASP cc_start: 0.7765 (m-30) cc_final: 0.7453 (m-30)
REVERT: A  234 SER cc_start: 0.8754 (t) cc_final: 0.8411 (p)
REVERT: A  285 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8141 (m)
REVERT: A  404 ASP cc_start: 0.8071 (m-30) cc_final: 0.7800 (t0)
REVERT: A  431 ILE cc_start: 0.8373 (mm) cc_final: 0.8149 (mt)
REVERT: A  503 MET cc_start: 0.8198 (mtp) cc_final: 0.7981 (mtm)
REVERT: A  526 TYR cc_start: 0.8553 (m-10) cc_final: 0.8127 (m-10)
REVERT: A  530 GLU cc_start: 0.7110 (pm20) cc_final: 0.6768 (pm20)
REVERT: A  569 ASN cc_start: 0.8766 (t0) cc_final: 0.8504 (t0)
REVERT: A  579 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7503 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7588 (m90) cc_final: 0.7346 (m90)
  outliers start: 17
  outliers final: 12
  residues processed: 192
  average time/residue: 0.0682
  time to fit residues: 17.8497
Evaluate side-chains
  199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9990
   chunk 72 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0370
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.4658

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.123091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.109244 restraints weight = 10261.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.62
r_work: 0.3395 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6372  Z= 0.139
  Angle     :  0.551  11.194   8657  Z= 0.281
  Chirality :  0.042   0.151    977
  Planarity :  0.004   0.059   1090
  Dihedral  :  7.926  73.198    940
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.57 %
    Favored  : 79.58 %
  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:  0.02 (0.30), residues: 766
  helix:  0.80 (0.31), residues: 294
  sheet:  0.35 (0.47), residues: 134
  loop : -0.76 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 151 
 TYR   0.014   0.001   TYR A 240 
 PHE   0.017   0.001   PHE A 235 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 6371)
  covalent geometry    : angle       0.55052 /  0.28 ( 8657)
  hydrogen bonds       : bond        0.04559 /  3.11 (  250)
  hydrogen bonds       : angle       4.32953 /  2.91 (  705)
  Misc. bond           : bond        0.00004 /  0.00 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 189
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ASN cc_start: 0.8151 (t0) cc_final: 0.7723 (t0)
REVERT: A  124 ASN cc_start: 0.8256 (t0) cc_final: 0.8009 (t0)
REVERT: A  137 MET cc_start: 0.7967 (ttm) cc_final: 0.7755 (ttm)
REVERT: A  159 ASP cc_start: 0.7891 (m-30) cc_final: 0.7555 (t0)
REVERT: A  185 ASP cc_start: 0.7774 (m-30) cc_final: 0.7452 (m-30)
REVERT: A  234 SER cc_start: 0.8743 (t) cc_final: 0.8391 (p)
REVERT: A  285 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8138 (m)
REVERT: A  404 ASP cc_start: 0.8066 (m-30) cc_final: 0.7797 (t0)
REVERT: A  431 ILE cc_start: 0.8372 (mm) cc_final: 0.8154 (mt)
REVERT: A  465 GLU cc_start: 0.7923 (tp30) cc_final: 0.7506 (tt0)
REVERT: A  503 MET cc_start: 0.8198 (mtp) cc_final: 0.7991 (mtm)
REVERT: A  505 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8522 (ttmm)
REVERT: A  526 TYR cc_start: 0.8595 (m-10) cc_final: 0.8183 (m-10)
REVERT: A  530 GLU cc_start: 0.7134 (pm20) cc_final: 0.6792 (pm20)
REVERT: A  569 ASN cc_start: 0.8756 (t0) cc_final: 0.8484 (t0)
REVERT: A  579 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7475 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7615 (m90) cc_final: 0.7349 (m90)
  outliers start: 19
  outliers final: 14
  residues processed: 192
  average time/residue: 0.0551
  time to fit residues: 14.4336
Evaluate side-chains
  199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 184
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0270
   chunk 18 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0670
   overall best weight:    0.2976

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.124289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.110358 restraints weight = 10253.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.62
r_work: 0.3411 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6372  Z= 0.110
  Angle     :  0.539  11.912   8657  Z= 0.272
  Chirality :  0.041   0.136    977
  Planarity :  0.004   0.066   1090
  Dihedral  :  7.818  73.222    940
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.47 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.31), residues: 766
  helix:  0.92 (0.31), residues: 292
  sheet:  0.36 (0.47), residues: 134
  loop : -0.77 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 434 
 TYR   0.012   0.001   TYR A 240 
 PHE   0.016   0.001   PHE A 235 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 ( 6371)
  covalent geometry    : angle       0.53870 /  0.27 ( 8657)
  hydrogen bonds       : bond        0.04182 /  2.86 (  250)
  hydrogen bonds       : angle       4.21665 /  2.83 (  705)
  Misc. bond           : bond        0.00006 /  0.00 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   65 ASP cc_start: 0.7640 (t0) cc_final: 0.7431 (t70)
REVERT: A   93 ASN cc_start: 0.8141 (t0) cc_final: 0.7714 (t0)
REVERT: A  124 ASN cc_start: 0.8230 (t0) cc_final: 0.7979 (t0)
REVERT: A  159 ASP cc_start: 0.7886 (m-30) cc_final: 0.7555 (t0)
REVERT: A  164 MET cc_start: 0.8510 (tpp) cc_final: 0.7579 (tpp)
REVERT: A  185 ASP cc_start: 0.7773 (m-30) cc_final: 0.7448 (m-30)
REVERT: A  234 SER cc_start: 0.8733 (t) cc_final: 0.8382 (p)
REVERT: A  284 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7293 (mm-40)
REVERT: A  285 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8137 (m)
REVERT: A  404 ASP cc_start: 0.8043 (m-30) cc_final: 0.7775 (t0)
REVERT: A  431 ILE cc_start: 0.8353 (mm) cc_final: 0.8135 (mt)
REVERT: A  503 MET cc_start: 0.8205 (mtp) cc_final: 0.7992 (mtm)
REVERT: A  505 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8516 (ttmm)
REVERT: A  526 TYR cc_start: 0.8577 (m-10) cc_final: 0.8221 (m-10)
REVERT: A  530 GLU cc_start: 0.7136 (pm20) cc_final: 0.6816 (pm20)
REVERT: A  575 LYS cc_start: 0.8798 (mttt) cc_final: 0.8537 (mttp)
REVERT: B  156 HIS cc_start: 0.7624 (m90) cc_final: 0.7367 (m90)
  outliers start: 19
  outliers final: 14
  residues processed: 189
  average time/residue: 0.0564
  time to fit residues: 14.5659
Evaluate side-chains
  196 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.4758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  71 ASN
A 539 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.123532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.109474 restraints weight = 10295.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.70
r_work: 0.3386 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6372  Z= 0.141
  Angle     :  0.558  11.557   8657  Z= 0.284
  Chirality :  0.042   0.140    977
  Planarity :  0.004   0.064   1090
  Dihedral  :  7.781  73.126    940
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.42 %
    Favored  : 76.73 %
  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:  0.05 (0.31), residues: 766
  helix:  0.83 (0.31), residues: 300
  sheet:  0.38 (0.47), residues: 134
  loop : -0.79 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 434 
 TYR   0.013   0.001   TYR A 240 
 PHE   0.017   0.001   PHE A 152 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 6371)
  covalent geometry    : angle       0.55783 /  0.28 ( 8657)
  hydrogen bonds       : bond        0.04388 /  3.00 (  250)
  hydrogen bonds       : angle       4.26839 /  2.87 (  705)
  Misc. bond           : bond        0.00002 /  0.00 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 ASP cc_start: 0.7672 (t0) cc_final: 0.7463 (t70)
REVERT: A   93 ASN cc_start: 0.8163 (t0) cc_final: 0.7730 (t0)
REVERT: A  159 ASP cc_start: 0.7898 (m-30) cc_final: 0.7554 (t0)
REVERT: A  162 ASN cc_start: 0.7631 (t0) cc_final: 0.7176 (t0)
REVERT: A  185 ASP cc_start: 0.7811 (m-30) cc_final: 0.7464 (m-30)
REVERT: A  234 SER cc_start: 0.8744 (t) cc_final: 0.8379 (p)
REVERT: A  285 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8174 (m)
REVERT: A  404 ASP cc_start: 0.8063 (m-30) cc_final: 0.7783 (t0)
REVERT: A  431 ILE cc_start: 0.8347 (mm) cc_final: 0.8138 (mt)
REVERT: A  465 GLU cc_start: 0.7957 (tp30) cc_final: 0.7589 (tt0)
REVERT: A  503 MET cc_start: 0.8212 (mtp) cc_final: 0.7993 (mtm)
REVERT: A  505 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8511 (ttmm)
REVERT: A  530 GLU cc_start: 0.7144 (pm20) cc_final: 0.6835 (pm20)
REVERT: A  569 ASN cc_start: 0.8739 (t0) cc_final: 0.8352 (t0)
REVERT: A  575 LYS cc_start: 0.8807 (mttt) cc_final: 0.8513 (mttp)
REVERT: B  156 HIS cc_start: 0.7648 (m90) cc_final: 0.7392 (m90)
  outliers start: 19
  outliers final: 15
  residues processed: 184
  average time/residue: 0.0630
  time to fit residues: 15.7181
Evaluate side-chains
  197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   71 ASN
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0000
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.122554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.108795 restraints weight = 10292.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.64
r_work: 0.3380 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6372  Z= 0.199
  Angle     :  0.595  12.207   8657  Z= 0.305
  Chirality :  0.044   0.184    977
  Planarity :  0.005   0.063   1090
  Dihedral  :  7.820  73.004    940
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.02 %
    Favored  : 76.58 %
  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:  0.04 (0.30), residues: 766
  helix:  0.84 (0.31), residues: 294
  sheet:  0.35 (0.47), residues: 134
  loop : -0.78 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 369 
 TYR   0.021   0.002   TYR A 240 
 PHE   0.029   0.002   PHE A 235 
 TRP   0.007   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00460 /  0.20 ( 6371)
  covalent geometry    : angle       0.59497 /  0.31 ( 8657)
  hydrogen bonds       : bond        0.04805 /  3.29 (  250)
  hydrogen bonds       : angle       4.39871 /  2.96 (  705)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 187
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 MET cc_start: 0.8035 (ttt) cc_final: 0.7639 (ttt)
REVERT: A   93 ASN cc_start: 0.8174 (t0) cc_final: 0.7747 (t0)
REVERT: A  124 ASN cc_start: 0.8286 (t0) cc_final: 0.8009 (t0)
REVERT: A  159 ASP cc_start: 0.7909 (m-30) cc_final: 0.7567 (t0)
REVERT: A  185 ASP cc_start: 0.7821 (m-30) cc_final: 0.7479 (m-30)
REVERT: A  234 SER cc_start: 0.8755 (t) cc_final: 0.8386 (p)
REVERT: A  285 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8160 (m)
REVERT: A  404 ASP cc_start: 0.8080 (m-30) cc_final: 0.7814 (t0)
REVERT: A  431 ILE cc_start: 0.8372 (mm) cc_final: 0.8163 (mt)
REVERT: A  465 GLU cc_start: 0.7966 (tp30) cc_final: 0.7542 (tt0)
REVERT: A  503 MET cc_start: 0.8230 (mtp) cc_final: 0.8022 (mtm)
REVERT: A  505 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8530 (ttmm)
REVERT: A  526 TYR cc_start: 0.8585 (m-10) cc_final: 0.8182 (m-10)
REVERT: A  530 GLU cc_start: 0.7153 (pm20) cc_final: 0.6896 (pm20)
REVERT: A  575 LYS cc_start: 0.8811 (mttt) cc_final: 0.8463 (mttm)
REVERT: B  156 HIS cc_start: 0.7687 (m90) cc_final: 0.7414 (m90)
  outliers start: 16
  outliers final: 13
  residues processed: 190
  average time/residue: 0.0619
  time to fit residues: 15.7930
Evaluate side-chains
  196 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 74 optimal weight:    0.2980
   chunk 76 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 69 optimal weight:    0.0370
   chunk 21 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0570
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.3176

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.123977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.110146 restraints weight = 10209.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.61
r_work: 0.3401 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6372  Z= 0.123
  Angle     :  0.577  12.971   8657  Z= 0.291
  Chirality :  0.041   0.182    977
  Planarity :  0.004   0.070   1090
  Dihedral  :  7.753  73.147    940
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.47 %
    Favored  : 76.28 %
  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:  0.12 (0.31), residues: 766
  helix:  0.93 (0.31), residues: 294
  sheet:  0.36 (0.47), residues: 134
  loop : -0.74 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 369 
 TYR   0.013   0.001   TYR A 240 
 PHE   0.025   0.002   PHE A 235 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 6371)
  covalent geometry    : angle       0.57701 /  0.29 ( 8657)
  hydrogen bonds       : bond        0.04357 /  2.94 (  250)
  hydrogen bonds       : angle       4.27196 /  2.86 (  705)
  Misc. bond           : bond        0.00008 /  0.00 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 MET cc_start: 0.8046 (ttt) cc_final: 0.7657 (ttt)
REVERT: A   93 ASN cc_start: 0.8150 (t0) cc_final: 0.7729 (t0)
REVERT: A  159 ASP cc_start: 0.7899 (m-30) cc_final: 0.7559 (t0)
REVERT: A  162 ASN cc_start: 0.7603 (t0) cc_final: 0.7210 (t0)
REVERT: A  164 MET cc_start: 0.8528 (tpp) cc_final: 0.7664 (tpp)
REVERT: A  185 ASP cc_start: 0.7778 (m-30) cc_final: 0.7439 (m-30)
REVERT: A  234 SER cc_start: 0.8748 (t) cc_final: 0.8392 (p)
REVERT: A  285 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8149 (m)
REVERT: A  404 ASP cc_start: 0.8058 (m-30) cc_final: 0.7789 (t0)
REVERT: A  431 ILE cc_start: 0.8349 (mm) cc_final: 0.8134 (mt)
REVERT: A  503 MET cc_start: 0.8216 (mtp) cc_final: 0.8013 (mtm)
REVERT: A  505 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8524 (ttmm)
REVERT: A  526 TYR cc_start: 0.8551 (m-10) cc_final: 0.8149 (m-10)
REVERT: A  530 GLU cc_start: 0.7152 (pm20) cc_final: 0.6927 (pm20)
REVERT: A  569 ASN cc_start: 0.8741 (t0) cc_final: 0.8356 (t0)
REVERT: B  156 HIS cc_start: 0.7632 (m90) cc_final: 0.7363 (m90)
  outliers start: 15
  outliers final: 14
  residues processed: 181
  average time/residue: 0.0680
  time to fit residues: 16.3852
Evaluate side-chains
  192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 177
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 49 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.123009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.109227 restraints weight = 10223.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.62
r_work: 0.3387 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6372  Z= 0.178
  Angle     :  0.592  12.241   8657  Z= 0.302
  Chirality :  0.043   0.175    977
  Planarity :  0.005   0.070   1090
  Dihedral  :  7.779  73.065    940
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.17 %
    Favored  : 76.58 %
  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:  0.06 (0.30), residues: 766
  helix:  0.86 (0.31), residues: 294
  sheet:  0.35 (0.47), residues: 134
  loop : -0.76 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 369 
 TYR   0.016   0.002   TYR A 240 
 PHE   0.027   0.002   PHE A 235 
 TRP   0.007   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.18 ( 6371)
  covalent geometry    : angle       0.59234 /  0.30 ( 8657)
  hydrogen bonds       : bond        0.04740 /  3.23 (  250)
  hydrogen bonds       : angle       4.34447 /  2.91 (  705)
  Misc. bond           : bond        0.00004 /  0.00 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1430.28 seconds
wall clock time: 25 minutes 14.84 seconds (1514.84 seconds total)