Starting phenix.real_space_refine
on Sat May 10 12:15:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_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_45380/05_2025/9ca4_45380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380_neut.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.24, per 1000 atoms: 0.68
  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: 1.43
  Conformation dependent library (CDL) restraints added in 772.1 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: 1.67
  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: 1.62

  Time building geometry restraints manager: 1.68 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: 731
       0.044 -    0.088: 179
       0.088 -    0.131: 55
       0.131 -    0.175: 10
       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 2.320
  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 2.320
  nonbonded pdb=" OD2 ASP A 511 "
            pdb="MN    MN A 701 "
     model   vdw
     2.168 2.320
  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:             3.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.050
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
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= 0.346
  Angle     :  0.870  37.956   8657  Z= 0.483
  Chirality :  0.044   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.008   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A  60 
 PHE   0.018   0.002   PHE A 265 
 TYR   0.016   0.002   TYR A 240 
 ARG   0.007   0.000   ARG A 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19650 (  250)
  hydrogen bonds       : angle       5.89950 (  705)
  covalent geometry    : bond        0.00464 ( 6371)
  covalent geometry    : angle       0.86963 ( 8657)
  Misc. bond           : bond        0.20258 (    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  : 0.707 
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: 0.8136 (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: 0.7465 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1660
  time to fit residues: 46.9432
Evaluate side-chains
  204 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.0050
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0980
   overall best weight:    0.4594

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.123775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.110027 restraints weight = 10143.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.56
r_work: 0.3398 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6372  Z= 0.146
  Angle     :  0.590  10.733   8657  Z= 0.303
  Chirality :  0.044   0.237    977
  Planarity :  0.005   0.061   1090
  Dihedral  :  8.276  73.437    940
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 14.41 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.30), residues: 766
  helix:  0.77 (0.30), residues: 292
  sheet:  0.47 (0.49), residues: 128
  loop : -0.88 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A  60 
 PHE   0.031   0.002   PHE A 214 
 TYR   0.014   0.001   TYR A 240 
 ARG   0.005   0.000   ARG A 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05001 (  250)
  hydrogen bonds       : angle       4.60052 (  705)
  covalent geometry    : bond        0.00329 ( 6371)
  covalent geometry    : angle       0.59012 ( 8657)
  Misc. bond           : bond        0.00005 (    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
  201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 195
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A   21 LEU cc_start: 0.8385 (tp) cc_final: 0.8154 (tt)
REVERT: A   48 GLN cc_start: 0.8042 (mp10) cc_final: 0.7702 (mp10)
REVERT: A   56 SER cc_start: 0.8508 (p) cc_final: 0.8290 (p)
REVERT: A   93 ASN cc_start: 0.8103 (t0) cc_final: 0.7855 (t0)
REVERT: A  124 ASN cc_start: 0.8207 (t0) cc_final: 0.7967 (t0)
REVERT: A  159 ASP cc_start: 0.7814 (m-30) cc_final: 0.7495 (t0)
REVERT: A  169 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7175 (mm-30)
REVERT: A  185 ASP cc_start: 0.7777 (m-30) cc_final: 0.7532 (m-30)
REVERT: A  234 SER cc_start: 0.8737 (t) cc_final: 0.8491 (p)
REVERT: A  284 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7138 (mm-40)
REVERT: A  306 MET cc_start: 0.8116 (ttp) cc_final: 0.7870 (ttp)
REVERT: A  431 ILE cc_start: 0.8374 (mm) cc_final: 0.8162 (mt)
REVERT: A  465 GLU cc_start: 0.8140 (tp30) cc_final: 0.7374 (tt0)
REVERT: A  503 MET cc_start: 0.8201 (mtp) cc_final: 0.7980 (mtm)
REVERT: A  526 TYR cc_start: 0.8598 (m-10) cc_final: 0.8196 (m-10)
REVERT: A  530 GLU cc_start: 0.7089 (pm20) cc_final: 0.6769 (pm20)
REVERT: A  569 ASN cc_start: 0.8797 (t0) cc_final: 0.8517 (t0)
REVERT: A  579 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.7614 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7545 (m-70) cc_final: 0.7341 (m90)
  outliers start: 6
  outliers final: 5
  residues processed: 195
  average time/residue: 0.1574
  time to fit residues: 40.9419
Evaluate side-chains
  192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 187
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain B residue   62 VAL
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 5 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0050
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
A 347 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.123462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.109555 restraints weight = 10147.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.59
r_work: 0.3393 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6372  Z= 0.150
  Angle     :  0.555   9.677   8657  Z= 0.285
  Chirality :  0.042   0.163    977
  Planarity :  0.005   0.058   1090
  Dihedral  :  7.981  73.166    940
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.32 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.30), residues: 766
  helix:  0.84 (0.31), residues: 294
  sheet:  0.58 (0.49), residues: 127
  loop : -0.82 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 415 
 PHE   0.026   0.002   PHE A 235 
 TYR   0.014   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04790 (  250)
  hydrogen bonds       : angle       4.42417 (  705)
  covalent geometry    : bond        0.00342 ( 6371)
  covalent geometry    : angle       0.55493 ( 8657)
  Misc. bond           : bond        0.00086 (    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
  207 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 192
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 LEU cc_start: 0.8447 (tp) cc_final: 0.8238 (tt)
REVERT: A   48 GLN cc_start: 0.8026 (mp10) cc_final: 0.7609 (mp10)
REVERT: A   56 SER cc_start: 0.8534 (p) cc_final: 0.8327 (p)
REVERT: A  124 ASN cc_start: 0.8213 (t0) cc_final: 0.7978 (t0)
REVERT: A  159 ASP cc_start: 0.7856 (m-30) cc_final: 0.7543 (t0)
REVERT: A  185 ASP cc_start: 0.7820 (m-30) cc_final: 0.7475 (m-30)
REVERT: A  234 SER cc_start: 0.8728 (t) cc_final: 0.8431 (p)
REVERT: A  284 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7229 (mm-40)
REVERT: A  404 ASP cc_start: 0.8037 (m-30) cc_final: 0.7754 (t0)
REVERT: A  431 ILE cc_start: 0.8392 (mm) cc_final: 0.8184 (mt)
REVERT: A  465 GLU cc_start: 0.8129 (tp30) cc_final: 0.7681 (tm-30)
REVERT: A  526 TYR cc_start: 0.8600 (m-10) cc_final: 0.8181 (m-10)
REVERT: A  530 GLU cc_start: 0.7124 (pm20) cc_final: 0.6912 (pm20)
REVERT: A  569 ASN cc_start: 0.8749 (t0) cc_final: 0.8476 (t0)
REVERT: A  579 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7617 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7591 (m-70) cc_final: 0.7330 (m90)
  outliers start: 15
  outliers final: 14
  residues processed: 193
  average time/residue: 0.1660
  time to fit residues: 42.6737
Evaluate side-chains
  200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   96 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  370 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
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  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 64 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0170
   chunk 75 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 63 optimal weight:    0.2980
   chunk 74 optimal weight:    0.0980
   overall best weight:    0.3618

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.124437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.110507 restraints weight = 10189.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.62
r_work: 0.3403 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6372  Z= 0.118
  Angle     :  0.529  11.145   8657  Z= 0.269
  Chirality :  0.041   0.210    977
  Planarity :  0.004   0.054   1090
  Dihedral  :  7.768  73.177    940
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.27 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.31), residues: 766
  helix:  0.97 (0.31), residues: 292
  sheet:  0.42 (0.47), residues: 134
  loop : -0.82 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 415 
 PHE   0.029   0.002   PHE A 214 
 TYR   0.012   0.001   TYR A 240 
 ARG   0.005   0.000   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  250)
  hydrogen bonds       : angle       4.24950 (  705)
  covalent geometry    : bond        0.00264 ( 6371)
  covalent geometry    : angle       0.52927 ( 8657)
  Misc. bond           : bond        0.00002 (    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
  207 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.7984 (mp10) cc_final: 0.7588 (mp10)
REVERT: A  124 ASN cc_start: 0.8229 (t0) cc_final: 0.7982 (t0)
REVERT: A  159 ASP cc_start: 0.7898 (m-30) cc_final: 0.7568 (t0)
REVERT: A  169 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7255 (mm-30)
REVERT: A  185 ASP cc_start: 0.7786 (m-30) cc_final: 0.7451 (m-30)
REVERT: A  232 ILE cc_start: 0.8616 (mm) cc_final: 0.8295 (tp)
REVERT: A  234 SER cc_start: 0.8724 (t) cc_final: 0.8396 (p)
REVERT: A  284 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7243 (mm-40)
REVERT: A  296 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7547 (mt0)
REVERT: A  404 ASP cc_start: 0.8014 (m-30) cc_final: 0.7760 (t0)
REVERT: A  431 ILE cc_start: 0.8366 (mm) cc_final: 0.8164 (mt)
REVERT: A  505 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8526 (ttmm)
REVERT: A  526 TYR cc_start: 0.8581 (m-10) cc_final: 0.8182 (m-10)
REVERT: A  530 GLU cc_start: 0.7141 (pm20) cc_final: 0.6906 (pm20)
REVERT: A  552 ASP cc_start: 0.7718 (t0) cc_final: 0.7433 (t0)
REVERT: A  579 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7587 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7585 (m-70) cc_final: 0.7331 (m90)
  outliers start: 13
  outliers final: 10
  residues processed: 197
  average time/residue: 0.1589
  time to fit residues: 42.3650
Evaluate side-chains
  196 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 186
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  478 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 60 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.123249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.109512 restraints weight = 10208.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.61
r_work: 0.3384 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6372  Z= 0.164
  Angle     :  0.550  10.913   8657  Z= 0.281
  Chirality :  0.042   0.187    977
  Planarity :  0.004   0.053   1090
  Dihedral  :  7.780  73.014    940
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.02 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.30), residues: 766
  helix:  0.88 (0.31), residues: 294
  sheet:  0.40 (0.47), residues: 134
  loop : -0.74 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 415 
 PHE   0.019   0.002   PHE A 214 
 TYR   0.016   0.002   TYR A 240 
 ARG   0.004   0.000   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  250)
  hydrogen bonds       : angle       4.28386 (  705)
  covalent geometry    : bond        0.00377 ( 6371)
  covalent geometry    : angle       0.55004 ( 8657)
  Misc. bond           : bond        0.00016 (    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
  202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.7947 (mp10) cc_final: 0.7729 (mp10)
REVERT: A  159 ASP cc_start: 0.7899 (m-30) cc_final: 0.7569 (t0)
REVERT: A  162 ASN cc_start: 0.7600 (t0) cc_final: 0.7271 (t0)
REVERT: A  185 ASP cc_start: 0.7783 (m-30) cc_final: 0.7436 (m-30)
REVERT: A  234 SER cc_start: 0.8734 (t) cc_final: 0.8398 (p)
REVERT: A  284 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7285 (mm-40)
REVERT: A  285 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8140 (m)
REVERT: A  306 MET cc_start: 0.7996 (ttp) cc_final: 0.7763 (ttp)
REVERT: A  404 ASP cc_start: 0.8045 (m-30) cc_final: 0.7801 (t0)
REVERT: A  431 ILE cc_start: 0.8372 (mm) cc_final: 0.8170 (mt)
REVERT: A  505 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8514 (ttmm)
REVERT: A  526 TYR cc_start: 0.8575 (m-10) cc_final: 0.8162 (m-10)
REVERT: A  530 GLU cc_start: 0.7096 (pm20) cc_final: 0.6795 (pm20)
REVERT: A  569 ASN cc_start: 0.8748 (t0) cc_final: 0.8371 (t0)
REVERT: A  579 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.7596 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7580 (m-70) cc_final: 0.7326 (m90)
  outliers start: 15
  outliers final: 11
  residues processed: 191
  average time/residue: 0.1727
  time to fit residues: 43.5908
Evaluate side-chains
  198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 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  430 THR
Chi-restraints excluded: chain A residue  439 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:    0.3980
   chunk 59 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0050
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.124242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.110532 restraints weight = 10201.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.59
r_work: 0.3410 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6372  Z= 0.119
  Angle     :  0.548  11.931   8657  Z= 0.273
  Chirality :  0.041   0.206    977
  Planarity :  0.004   0.064   1090
  Dihedral  :  7.714  73.147    940
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.82 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.31), residues: 766
  helix:  0.98 (0.31), residues: 292
  sheet:  0.42 (0.47), residues: 134
  loop : -0.73 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 415 
 PHE   0.023   0.001   PHE A 214 
 TYR   0.013   0.001   TYR A 240 
 ARG   0.004   0.000   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04185 (  250)
  hydrogen bonds       : angle       4.16217 (  705)
  covalent geometry    : bond        0.00270 ( 6371)
  covalent geometry    : angle       0.54848 ( 8657)
  Misc. bond           : bond        0.00005 (    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
  207 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.7907 (mp10) cc_final: 0.7483 (mp10)
REVERT: A   93 ASN cc_start: 0.8168 (t0) cc_final: 0.7775 (t0)
REVERT: A  159 ASP cc_start: 0.7907 (m-30) cc_final: 0.7544 (t0)
REVERT: A  162 ASN cc_start: 0.7575 (t0) cc_final: 0.7237 (t0)
REVERT: A  185 ASP cc_start: 0.7761 (m-30) cc_final: 0.7412 (m-30)
REVERT: A  234 SER cc_start: 0.8715 (t) cc_final: 0.8390 (p)
REVERT: A  284 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7282 (mm-40)
REVERT: A  285 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8154 (m)
REVERT: A  404 ASP cc_start: 0.7994 (m-30) cc_final: 0.7748 (t0)
REVERT: A  431 ILE cc_start: 0.8357 (mm) cc_final: 0.8150 (mt)
REVERT: A  505 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8532 (ttmm)
REVERT: A  526 TYR cc_start: 0.8569 (m-10) cc_final: 0.8176 (m-10)
REVERT: A  530 GLU cc_start: 0.7116 (pm20) cc_final: 0.6808 (pm20)
REVERT: A  569 ASN cc_start: 0.8741 (t0) cc_final: 0.8359 (t0)
REVERT: A  579 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.7567 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7572 (m-70) cc_final: 0.7314 (m90)
  outliers start: 18
  outliers final: 12
  residues processed: 195
  average time/residue: 0.1766
  time to fit residues: 45.9779
Evaluate side-chains
  201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 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  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  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 51 optimal weight:    0.0170
   chunk 61 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    0.3980
   chunk 43 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.3176

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.125178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.111434 restraints weight = 10238.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 2.61
r_work: 0.3422 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6372  Z= 0.111
  Angle     :  0.539  12.055   8657  Z= 0.269
  Chirality :  0.041   0.200    977
  Planarity :  0.004   0.061   1090
  Dihedral  :  7.633  73.168    940
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.31), residues: 766
  helix:  1.08 (0.31), residues: 292
  sheet:  0.50 (0.47), residues: 134
  loop : -0.65 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A  60 
 PHE   0.028   0.002   PHE A 235 
 TYR   0.012   0.001   TYR A 240 
 ARG   0.002   0.000   ARG A 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03961 (  250)
  hydrogen bonds       : angle       4.10571 (  705)
  covalent geometry    : bond        0.00251 ( 6371)
  covalent geometry    : angle       0.53939 ( 8657)
  Misc. bond           : bond        0.00003 (    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
  200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 182
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.7883 (mp10) cc_final: 0.7458 (mp10)
REVERT: A   54 MET cc_start: 0.7998 (ttt) cc_final: 0.7666 (ttt)
REVERT: A   93 ASN cc_start: 0.8169 (t0) cc_final: 0.7773 (t0)
REVERT: A  134 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8635 (mp)
REVERT: A  159 ASP cc_start: 0.7876 (m-30) cc_final: 0.7531 (t0)
REVERT: A  162 ASN cc_start: 0.7564 (t0) cc_final: 0.7227 (t0)
REVERT: A  185 ASP cc_start: 0.7730 (m-30) cc_final: 0.7367 (m-30)
REVERT: A  234 SER cc_start: 0.8709 (t) cc_final: 0.8348 (p)
REVERT: A  284 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7369 (mm-40)
REVERT: A  285 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8149 (m)
REVERT: A  306 MET cc_start: 0.8019 (ttp) cc_final: 0.7768 (ttp)
REVERT: A  404 ASP cc_start: 0.8038 (m-30) cc_final: 0.7791 (t0)
REVERT: A  431 ILE cc_start: 0.8357 (mm) cc_final: 0.8155 (mt)
REVERT: A  505 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8495 (ttmm)
REVERT: A  526 TYR cc_start: 0.8572 (m-10) cc_final: 0.8242 (m-10)
REVERT: A  530 GLU cc_start: 0.7174 (pm20) cc_final: 0.6878 (pm20)
REVERT: A  569 ASN cc_start: 0.8744 (t0) cc_final: 0.8346 (t0)
REVERT: A  579 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7570 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7467 (m-70) cc_final: 0.7198 (m90)
  outliers start: 18
  outliers final: 12
  residues processed: 187
  average time/residue: 0.1663
  time to fit residues: 41.6674
Evaluate side-chains
  192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 178
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
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  134 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  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  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0010
   overall best weight:    0.5186

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.123912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.110145 restraints weight = 10184.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.62
r_work: 0.3399 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6372  Z= 0.148
  Angle     :  0.553  12.493   8657  Z= 0.279
  Chirality :  0.042   0.186    977
  Planarity :  0.004   0.058   1090
  Dihedral  :  7.610  73.063    940
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.87 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.31), residues: 766
  helix:  0.99 (0.31), residues: 294
  sheet:  0.44 (0.47), residues: 134
  loop : -0.62 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 415 
 PHE   0.028   0.002   PHE A 235 
 TYR   0.015   0.001   TYR A 240 
 ARG   0.007   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04430 (  250)
  hydrogen bonds       : angle       4.15653 (  705)
  covalent geometry    : bond        0.00340 ( 6371)
  covalent geometry    : angle       0.55346 ( 8657)
  Misc. bond           : bond        0.00011 (    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: 18
    poor density    : 180
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.7889 (mp10) cc_final: 0.7455 (mp10)
REVERT: A   54 MET cc_start: 0.8004 (ttt) cc_final: 0.7649 (ttt)
REVERT: A   93 ASN cc_start: 0.8190 (t0) cc_final: 0.7785 (t0)
REVERT: A  145 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7776 (tttt)
REVERT: A  159 ASP cc_start: 0.7881 (m-30) cc_final: 0.7556 (t0)
REVERT: A  162 ASN cc_start: 0.7590 (t0) cc_final: 0.7132 (t0)
REVERT: A  185 ASP cc_start: 0.7781 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  234 SER cc_start: 0.8722 (t) cc_final: 0.8362 (p)
REVERT: A  284 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7389 (mm-40)
REVERT: A  285 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8159 (m)
REVERT: A  306 MET cc_start: 0.7972 (ttp) cc_final: 0.7729 (ttp)
REVERT: A  404 ASP cc_start: 0.8076 (m-30) cc_final: 0.7827 (t0)
REVERT: A  431 ILE cc_start: 0.8354 (mm) cc_final: 0.8149 (mt)
REVERT: A  505 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8515 (ttmm)
REVERT: A  526 TYR cc_start: 0.8616 (m-10) cc_final: 0.8301 (m-10)
REVERT: A  530 GLU cc_start: 0.7116 (pm20) cc_final: 0.6808 (pm20)
REVERT: A  569 ASN cc_start: 0.8772 (t0) cc_final: 0.8356 (t0)
REVERT: A  575 LYS cc_start: 0.8774 (mttt) cc_final: 0.8471 (mttm)
REVERT: A  579 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7631 (mmm-85)
REVERT: B  111 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7187 (m-80)
REVERT: B  156 HIS cc_start: 0.7521 (m-70) cc_final: 0.7283 (m-70)
  outliers start: 18
  outliers final: 13
  residues processed: 186
  average time/residue: 0.1857
  time to fit residues: 45.7349
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  : 0.619 
-------------------------------------------------------------------------------
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  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  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  111 PHE
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 51 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0030
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0060
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0970
   chunk 66 optimal weight:    0.0040
   chunk 50 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.0616

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.127391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.113435 restraints weight = 10395.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.67
r_work: 0.3464 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6372  Z= 0.095
  Angle     :  0.546  12.346   8657  Z= 0.272
  Chirality :  0.040   0.209    977
  Planarity :  0.004   0.068   1090
  Dihedral  :  7.615  73.345    940
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 21.92 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.31), residues: 766
  helix:  1.08 (0.31), residues: 302
  sheet:  0.59 (0.48), residues: 134
  loop : -0.62 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 172 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.011   0.001   TYR A 411 
 ARG   0.007   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03399 (  250)
  hydrogen bonds       : angle       3.93494 (  705)
  covalent geometry    : bond        0.00206 ( 6371)
  covalent geometry    : angle       0.54576 ( 8657)
  Misc. bond           : bond        0.00001 (    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
  193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 182
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.7883 (mp10) cc_final: 0.7455 (mp10)
REVERT: A   54 MET cc_start: 0.7926 (ttt) cc_final: 0.7574 (ttt)
REVERT: A   93 ASN cc_start: 0.8154 (t0) cc_final: 0.7770 (t0)
REVERT: A  105 GLU cc_start: 0.7511 (tp30) cc_final: 0.7212 (tp30)
REVERT: A  134 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8695 (mp)
REVERT: A  159 ASP cc_start: 0.7828 (m-30) cc_final: 0.7486 (t0)
REVERT: A  162 ASN cc_start: 0.7526 (t0) cc_final: 0.7171 (t0)
REVERT: A  185 ASP cc_start: 0.7634 (m-30) cc_final: 0.7266 (m-30)
REVERT: A  234 SER cc_start: 0.8676 (t) cc_final: 0.8307 (p)
REVERT: A  284 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7479 (mm-40)
REVERT: A  285 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8202 (m)
REVERT: A  404 ASP cc_start: 0.7993 (m-30) cc_final: 0.7624 (t0)
REVERT: A  431 ILE cc_start: 0.8299 (mm) cc_final: 0.8087 (mt)
REVERT: A  526 TYR cc_start: 0.8563 (m-10) cc_final: 0.8225 (m-10)
REVERT: A  530 GLU cc_start: 0.7163 (pm20) cc_final: 0.6932 (pm20)
REVERT: A  569 ASN cc_start: 0.8738 (t0) cc_final: 0.8319 (t0)
REVERT: A  575 LYS cc_start: 0.8695 (mttt) cc_final: 0.8380 (mttm)
REVERT: A  579 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7424 (mmm-85)
  outliers start: 11
  outliers final: 9
  residues processed: 184
  average time/residue: 0.1857
  time to fit residues: 45.6728
Evaluate side-chains
  188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 177
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  227 GLU
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0770
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.124108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.110329 restraints weight = 10345.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.66
r_work: 0.3396 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6372  Z= 0.168
  Angle     :  0.586  12.455   8657  Z= 0.295
  Chirality :  0.043   0.184    977
  Planarity :  0.005   0.069   1090
  Dihedral  :  7.609  73.056    940
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 22.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.31), residues: 766
  helix:  1.02 (0.31), residues: 298
  sheet:  0.46 (0.47), residues: 134
  loop : -0.61 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 415 
 PHE   0.027   0.002   PHE A 235 
 TYR   0.014   0.002   TYR A 240 
 ARG   0.007   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04470 (  250)
  hydrogen bonds       : angle       4.12964 (  705)
  covalent geometry    : bond        0.00389 ( 6371)
  covalent geometry    : angle       0.58568 ( 8657)
  Misc. bond           : bond        0.00032 (    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
  193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 182
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.7840 (mp10) cc_final: 0.7379 (mp10)
REVERT: A   54 MET cc_start: 0.8001 (ttt) cc_final: 0.7651 (ttt)
REVERT: A   93 ASN cc_start: 0.8194 (t0) cc_final: 0.7804 (t0)
REVERT: A  105 GLU cc_start: 0.7553 (tp30) cc_final: 0.7256 (tp30)
REVERT: A  134 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8645 (mp)
REVERT: A  159 ASP cc_start: 0.7871 (m-30) cc_final: 0.7542 (t0)
REVERT: A  162 ASN cc_start: 0.7558 (t0) cc_final: 0.7102 (t0)
REVERT: A  185 ASP cc_start: 0.7815 (m-30) cc_final: 0.7464 (m-30)
REVERT: A  234 SER cc_start: 0.8716 (t) cc_final: 0.8356 (p)
REVERT: A  284 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7412 (mm-40)
REVERT: A  285 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8184 (m)
REVERT: A  404 ASP cc_start: 0.8140 (m-30) cc_final: 0.7859 (t0)
REVERT: A  431 ILE cc_start: 0.8356 (mm) cc_final: 0.8152 (mt)
REVERT: A  526 TYR cc_start: 0.8628 (m-10) cc_final: 0.8298 (m-10)
REVERT: A  530 GLU cc_start: 0.7183 (pm20) cc_final: 0.6871 (pm20)
REVERT: A  569 ASN cc_start: 0.8763 (t0) cc_final: 0.8374 (t0)
REVERT: A  575 LYS cc_start: 0.8741 (mttt) cc_final: 0.8418 (mttm)
REVERT: A  579 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7630 (mmm-85)
  outliers start: 11
  outliers final: 8
  residues processed: 186
  average time/residue: 0.1820
  time to fit residues: 44.6567
Evaluate side-chains
  191 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 181
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  227 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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 74 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.122792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.109281 restraints weight = 10370.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.64
r_work: 0.3380 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6372  Z= 0.189
  Angle     :  0.605  12.507   8657  Z= 0.305
  Chirality :  0.044   0.214    977
  Planarity :  0.005   0.067   1090
  Dihedral  :  7.717  75.709    940
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 22.52 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.31), residues: 766
  helix:  0.82 (0.30), residues: 299
  sheet:  0.28 (0.46), residues: 134
  loop : -0.63 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 415 
 PHE   0.029   0.002   PHE A 235 
 TYR   0.017   0.002   TYR A 240 
 ARG   0.007   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 (  250)
  hydrogen bonds       : angle       4.25734 (  705)
  covalent geometry    : bond        0.00435 ( 6371)
  covalent geometry    : angle       0.60493 ( 8657)
  Misc. bond           : bond        0.00031 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3235.35 seconds
wall clock time: 56 minutes 46.17 seconds (3406.17 seconds total)