Starting phenix.real_space_refine
on Tue Jan 14 08:37:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ca1_45379/01_2025/9ca1_45379_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ca1_45379/01_2025/9ca1_45379.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ca1_45379/01_2025/9ca1_45379.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ca1_45379/01_2025/9ca1_45379.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ca1_45379/01_2025/9ca1_45379_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ca1_45379/01_2025/9ca1_45379_neut.cif"
  }
  resolution = 3.26
  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      10      5.49       5
     S      40      5.16       5
     C    3927      2.51       5
     N    1080      2.21       5
     O    1206      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6265
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4844
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 30, 'TRANS': 581}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          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: "D"
      Number of atoms: 143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 143
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
    Chain: "E"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Classifications: {'DNA': 3}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 2}
          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: 4.59, per 1000 atoms: 0.73
  Number of scatterers: 6265
  At special positions: 0
  Unit cell: (71.38, 87.98, 136.12, 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      40     16.00
     P      10     15.00
     O    1206      8.00
     N    1080      7.00
     C    3927      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: 1.71
  Conformation dependent library (CDL) restraints added in 887.5 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:
      26 helices and 5 sheets defined
      41.9% alpha, 16.3% beta
      0 base pairs and 5 stacking pairs defined.
    Time for finding SS restraints: 1.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 22
    Processing helix  chain 'A' and resid 97 through 106
    Processing helix  chain 'A' and resid 119 through 134
      removed outlier: 4.184A  pdb=" N   GLU A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ASN A 124 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 157 through 166
    Processing helix  chain 'A' and resid 171 through 204
      removed outlier: 4.228A  pdb=" N   ALA A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA A 191 " --> pdb=" O   ARG A 187 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ARG A 194 " --> pdb=" O   CYS A 190 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A 195 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLY A 202 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   TYR A 204 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 234
      removed outlier: 3.665A  pdb=" N   CYS A 225 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 252
      removed outlier: 3.775A  pdb=" N   ASP A 252 " --> pdb=" O   THR A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 252'
    Processing helix  chain 'A' and resid 266 through 279
      removed outlier: 4.639A  pdb=" N   LEU A 279 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 313
    Processing helix  chain 'A' and resid 317 through 332
    Processing helix  chain 'A' and resid 349 through 357
      removed outlier: 4.060A  pdb=" N   GLN A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 374
    Processing helix  chain 'A' and resid 404 through 421
      removed outlier: 4.249A  pdb=" N   LEU A 408 " --> pdb=" O   ASP A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 455
      removed outlier: 3.757A  pdb=" N   GLU A 454 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 507
    Processing helix  chain 'A' and resid 513 through 524
    Processing helix  chain 'A' and resid 538 through 552
    Processing helix  chain 'A' and resid 553 through 556
    Processing helix  chain 'A' and resid 559 through 573
      removed outlier: 3.764A  pdb=" N   LEU A 570 " --> pdb=" O   LYS A 566 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   ILE A 571 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 598
      removed outlier: 3.845A  pdb=" N   ASP A 598 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 611
      removed outlier: 4.013A  pdb=" N   LEU A 606 " --> pdb=" O   GLY A 602 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   VAL A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
      removed outlier: 3.651A  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 17 through 25
    Processing helix  chain 'B' and resid 32 through 42
      removed outlier: 4.064A  pdb=" N   ASN B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 161
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30
      removed outlier: 6.019A  pdb=" N   SER A  37 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER A  56 " --> pdb=" O   SER A  37 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR A  41 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   VAL A   4 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   THR A  55 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   MET A   6 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   THR A   3 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   VAL A 113 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   LEU A   5 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   TRP A 115 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   VAL A   7 " --> pdb=" O   TRP A 115 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66
    Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 476
      removed outlier: 5.580A  pdb=" N   VAL A 285 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ARG A 434 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ALA A 287 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR A 426 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LYS A 425 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE A 435 " --> pdb=" O   GLU A 438 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLU A 438 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   SER A 443 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
      removed outlier: 8.563A  pdb=" N   LEU A 256 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   ALA A 245 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   TRP A 259 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   LEU A 243 " --> pdb=" O   TRP A 259 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS A 246 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   GLU A 480 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 530
      removed outlier: 3.649A  pdb=" N   ARG A 534 " --> pdb=" O   GLU A 530 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 66
      removed outlier: 4.400A  pdb=" N   ASP B 134 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 9.523A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   THR B 107 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   LEU B 142 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   LEU B  95 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ARG B  96 " --> pdb=" O   ILE B  76 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   ILE B  76 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   GLN B  98 " --> pdb=" O   GLN B  74 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   LYS B 126 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)

    268 hydrogen bonds defined for protein.
    768 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      5 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 1.96 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: 1861
        1.33 -     1.45: 1001
        1.45 -     1.57: 3468
        1.57 -     1.69: 17
        1.69 -     1.81: 63
  Bond restraints: 6410
  Sorted by residual:
  bond pdb=" OH  PTR A 336 "
       pdb=" P   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.769  1.607  0.162 2.00e-02 2.50e+03 6.56e+01
  bond pdb=" O3'  DA D   2 "
       pdb=" P    DA D   3 "
    ideal  model  delta    sigma   weight residual
    1.607  1.562  0.045 1.50e-02 4.44e+03 9.05e+00
  bond pdb=" O1P PTR A 336 "
       pdb=" P   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.522  1.480  0.042 2.00e-02 2.50e+03 4.48e+00
  bond pdb=" N   TRP A  73 "
       pdb=" CA  TRP A  73 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 1.29e-02 6.01e+03 4.29e+00
  bond pdb=" CZ  PTR A 336 "
       pdb=" OH  PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.339  1.301  0.038 2.00e-02 2.50e+03 3.66e+00
  ... (remaining 6405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 8562
        1.96 -     3.93: 129
        3.93 -     5.89: 19
        5.89 -     7.85: 2
        7.85 -     9.82: 2
  Bond angle restraints: 8714
  Sorted by residual:
  angle pdb=" N   VAL A 455 "
        pdb=" CA  VAL A 455 "
        pdb=" C   VAL A 455 "
      ideal   model   delta    sigma   weight residual
     112.96  109.10    3.86 1.00e+00 1.00e+00 1.49e+01
  angle pdb=" OH  PTR A 336 "
        pdb=" P   PTR A 336 "
        pdb=" O2P PTR A 336 "
      ideal   model   delta    sigma   weight residual
      99.92  109.47   -9.55 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" N   GLN B  11 "
        pdb=" CA  GLN B  11 "
        pdb=" CB  GLN B  11 "
      ideal   model   delta    sigma   weight residual
     110.39  115.56   -5.17 1.66e+00 3.63e-01 9.71e+00
  angle pdb=" CA  LEU B  41 "
        pdb=" CB  LEU B  41 "
        pdb=" CG  LEU B  41 "
      ideal   model   delta    sigma   weight residual
     116.30  126.12   -9.82 3.50e+00 8.16e-02 7.87e+00
  angle pdb=" C   SER B  10 "
        pdb=" N   GLN B  11 "
        pdb=" CA  GLN B  11 "
      ideal   model   delta    sigma   weight residual
     120.72  116.16    4.56 1.67e+00 3.59e-01 7.44e+00
  ... (remaining 8709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 3398
       17.90 -    35.80: 377
       35.80 -    53.70: 80
       53.70 -    71.60: 14
       71.60 -    89.50: 8
  Dihedral angle restraints: 3877
    sinusoidal: 1643
      harmonic: 2234
  Sorted by residual:
  dihedral pdb=" CD  ARG A 181 "
           pdb=" NE  ARG A 181 "
           pdb=" CZ  ARG A 181 "
           pdb=" NH1 ARG A 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   41.83  -41.83     1      1.00e+01 1.00e-02 2.45e+01
  dihedral pdb=" CB  GLU A 340 "
           pdb=" CG  GLU A 340 "
           pdb=" CD  GLU A 340 "
           pdb=" OE1 GLU A 340 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.50   89.50     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU B  22 "
           pdb=" CG  GLU B  22 "
           pdb=" CD  GLU B  22 "
           pdb=" OE1 GLU B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.51  -87.51     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 3874 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 574
       0.027 -    0.054: 244
       0.054 -    0.082: 106
       0.082 -    0.109: 35
       0.109 -    0.136: 18
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  ILE A 435 "
            pdb=" N   ILE A 435 "
            pdb=" C   ILE A 435 "
            pdb=" CB  ILE A 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  PTR A 336 "
            pdb=" N   PTR A 336 "
            pdb=" C   PTR A 336 "
            pdb=" CB  PTR A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.48   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  PRO A 457 "
            pdb=" N   PRO A 457 "
            pdb=" C   PRO A 457 "
            pdb=" CB  PRO A 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 974 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 181 "   -0.731 9.50e-02 1.11e+02   3.27e-01 6.53e+01
        pdb=" NE  ARG A 181 "    0.043 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 181 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 181 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 181 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 476 "    0.035 5.00e-02 4.00e+02   5.34e-02 4.56e+00
        pdb=" N   PRO A 477 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 477 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 477 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  77 "   -0.028 5.00e-02 4.00e+02   4.19e-02 2.81e+00
        pdb=" N   PRO A  78 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A  78 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  78 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 103
        2.68 -     3.23: 5725
        3.23 -     3.79: 8978
        3.79 -     4.34: 11810
        4.34 -     4.90: 19824
  Nonbonded interactions: 46440
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 511 "
            pdb="MN    MN A 702 "
     model   vdw
     2.120 2.320
  nonbonded pdb=" OE1 GLU A 340 "
            pdb="MN    MN A 702 "
     model   vdw
     2.124 2.320
  nonbonded pdb=" OD2 ASP A 117 "
            pdb="MN    MN A 701 "
     model   vdw
     2.130 2.320
  nonbonded pdb=" O3'  DA D   4 "
            pdb="MN    MN A 701 "
     model   vdw
     2.144 2.320
  nonbonded pdb=" OE2 GLU A   9 "
            pdb="MN    MN A 701 "
     model   vdw
     2.152 2.320
  ... (remaining 46435 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:             1.790
  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:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.000
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
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      :  0.004   0.162   6410  Z= 0.211
  Angle     :  0.593   9.818   8714  Z= 0.310
  Chirality :  0.040   0.136    977
  Planarity :  0.011   0.327   1092
  Dihedral  : 15.560  89.505   2435
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.18 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.28 (0.31), residues: 766
  helix:  1.31 (0.31), residues: 299
  sheet:  0.44 (0.49), residues: 121
  loop : -0.90 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 141 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.010   0.001   TYR A 578 
 ARG   0.002   0.000   ARG A  51 

*********************** 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
  212 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 CYS cc_start: 0.7358 (t) cc_final: 0.7048 (t)
REVERT: A  274 LEU cc_start: 0.8604 (tp) cc_final: 0.8385 (tt)
REVERT: A  474 ASP cc_start: 0.7758 (m-30) cc_final: 0.7405 (m-30)
REVERT: A  579 ARG cc_start: 0.6885 (mmp-170) cc_final: 0.6635 (mmp-170)
REVERT: B  150 LEU cc_start: 0.8379 (mm) cc_final: 0.8173 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2241
  time to fit residues: 59.3990
Evaluate side-chains
  197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    0.2980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.111455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.099173 restraints weight = 9628.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.36
r_work: 0.3120 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.0908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6410  Z= 0.278
  Angle     :  0.546   7.796   8714  Z= 0.291
  Chirality :  0.042   0.151    977
  Planarity :  0.004   0.051   1092
  Dihedral  : 10.676  79.026    950
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.66 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.24 %
    Favored  : 87.11 %
  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:  0.23 (0.30), residues: 766
  helix:  1.30 (0.31), residues: 301
  sheet:  0.19 (0.47), residues: 127
  loop : -0.89 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 363 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.012   0.002   PHE A 127 
 TYR   0.013   0.001   TYR A 426 
 ARG   0.005   0.000   ARG A 369 

*********************** 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
  208 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 197
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.8248 (tt) cc_final: 0.8039 (tp)
REVERT: A   84 GLN cc_start: 0.8049 (tt0) cc_final: 0.7721 (tt0)
REVERT: A  145 LYS cc_start: 0.8384 (ptmt) cc_final: 0.7900 (ptmt)
REVERT: A  166 CYS cc_start: 0.8196 (t) cc_final: 0.7907 (t)
REVERT: A  274 LEU cc_start: 0.8680 (tp) cc_final: 0.8439 (tt)
REVERT: A  425 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8231 (mttp)
REVERT: A  474 ASP cc_start: 0.8321 (m-30) cc_final: 0.8109 (m-30)
REVERT: A  510 THR cc_start: 0.8232 (m) cc_final: 0.7834 (p)
REVERT: A  579 ARG cc_start: 0.7348 (mmp-170) cc_final: 0.7121 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8581 (mm) cc_final: 0.8197 (mm)
  outliers start: 11
  outliers final: 8
  residues processed: 200
  average time/residue: 0.2307
  time to fit residues: 57.4579
Evaluate side-chains
  201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 193
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   27 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0270
   chunk 58 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0570
   chunk 37 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 62 optimal weight:    0.2980
   chunk 55 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.3356

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.112792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.100407 restraints weight = 9724.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.38
r_work: 0.3122 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6410  Z= 0.182
  Angle     :  0.514   7.886   8714  Z= 0.273
  Chirality :  0.040   0.137    977
  Planarity :  0.004   0.054   1092
  Dihedral  : 10.757  76.797    950
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.13 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.19 %
    Favored  : 84.41 %
  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:  0.34 (0.31), residues: 766
  helix:  1.45 (0.31), residues: 301
  sheet:  0.19 (0.48), residues: 122
  loop : -0.86 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 458 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.012   0.001   PHE A 214 
 TYR   0.011   0.001   TYR A 426 
 ARG   0.002   0.000   ARG A 591 

*********************** 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
  212 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.8253 (tt) cc_final: 0.8016 (tp)
REVERT: A   84 GLN cc_start: 0.8010 (tt0) cc_final: 0.7542 (tt0)
REVERT: A  145 LYS cc_start: 0.8365 (ptmt) cc_final: 0.7967 (ptmt)
REVERT: A  166 CYS cc_start: 0.8111 (t) cc_final: 0.7755 (t)
REVERT: A  231 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8524 (tttp)
REVERT: A  274 LEU cc_start: 0.8628 (tp) cc_final: 0.8393 (tt)
REVERT: A  425 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8183 (mttm)
REVERT: A  474 ASP cc_start: 0.8335 (m-30) cc_final: 0.8108 (m-30)
REVERT: A  510 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7865 (p)
REVERT: A  552 ASP cc_start: 0.7747 (t0) cc_final: 0.7442 (t0)
REVERT: A  579 ARG cc_start: 0.7328 (mmp-170) cc_final: 0.7077 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8134 (mm)
REVERT: B   11 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7643 (pm20)
  outliers start: 16
  outliers final: 8
  residues processed: 199
  average time/residue: 0.2272
  time to fit residues: 56.5140
Evaluate side-chains
  201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 189
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   47 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0770
   chunk 11 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.2980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.111815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.099343 restraints weight = 9826.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.40
r_work: 0.3109 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6410  Z= 0.226
  Angle     :  0.521   8.329   8714  Z= 0.277
  Chirality :  0.041   0.135    977
  Planarity :  0.004   0.053   1092
  Dihedral  : 10.752  75.164    950
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.39 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.44 %
    Favored  : 82.16 %
  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:  0.37 (0.31), residues: 766
  helix:  1.51 (0.31), residues: 301
  sheet:  0.15 (0.48), residues: 127
  loop : -0.86 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.012   0.001   PHE A 127 
 TYR   0.013   0.001   TYR A 426 
 ARG   0.006   0.000   ARG A 369 

*********************** 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
  211 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 195
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.8278 (tt) cc_final: 0.8038 (tp)
REVERT: A   84 GLN cc_start: 0.8051 (tt0) cc_final: 0.7653 (tt0)
REVERT: A  145 LYS cc_start: 0.8380 (ptmt) cc_final: 0.7990 (ptmt)
REVERT: A  166 CYS cc_start: 0.8132 (t) cc_final: 0.7789 (t)
REVERT: A  231 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8528 (ttmm)
REVERT: A  425 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8244 (mttm)
REVERT: A  474 ASP cc_start: 0.8357 (m-30) cc_final: 0.8131 (m-30)
REVERT: A  510 THR cc_start: 0.8272 (m) cc_final: 0.7887 (p)
REVERT: A  552 ASP cc_start: 0.7789 (t0) cc_final: 0.7565 (t0)
REVERT: A  567 GLN cc_start: 0.7796 (tp40) cc_final: 0.7240 (tp40)
REVERT: A  579 ARG cc_start: 0.7363 (mmp-170) cc_final: 0.7114 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8120 (mm)
REVERT: B   11 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7658 (pm20)
  outliers start: 16
  outliers final: 10
  residues processed: 198
  average time/residue: 0.2297
  time to fit residues: 56.5629
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  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  115 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0470
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0770
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   overall best weight:    0.3236

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.112700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.099955 restraints weight = 9733.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.44
r_work: 0.3118 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6410  Z= 0.173
  Angle     :  0.509   8.506   8714  Z= 0.268
  Chirality :  0.040   0.135    977
  Planarity :  0.004   0.051   1092
  Dihedral  : 10.730  73.783    950
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.39 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.04 %
    Favored  : 80.66 %
  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:  0.39 (0.31), residues: 766
  helix:  1.55 (0.31), residues: 301
  sheet:  0.14 (0.48), residues: 122
  loop : -0.85 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.012   0.001   PHE A 265 
 TYR   0.010   0.001   TYR A 411 
 ARG   0.006   0.000   ARG A 369 

*********************** 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
  213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 191
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6488 (m) cc_final: 0.5658 (p)
REVERT: A   26 LEU cc_start: 0.8208 (tt) cc_final: 0.7895 (tp)
REVERT: A   84 GLN cc_start: 0.7796 (tt0) cc_final: 0.7334 (tt0)
REVERT: A  145 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7976 (ptmt)
REVERT: A  166 CYS cc_start: 0.7887 (t) cc_final: 0.7488 (t)
REVERT: A  231 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8282 (ttmm)
REVERT: A  280 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7270 (mt-10)
REVERT: A  425 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8132 (mttm)
REVERT: A  474 ASP cc_start: 0.8097 (m-30) cc_final: 0.7895 (m-30)
REVERT: A  510 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7856 (p)
REVERT: A  552 ASP cc_start: 0.7580 (t0) cc_final: 0.7258 (t0)
REVERT: A  579 ARG cc_start: 0.7141 (mmp-170) cc_final: 0.6865 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8023 (mm)
REVERT: B   11 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7535 (pm20)
  outliers start: 22
  outliers final: 13
  residues processed: 195
  average time/residue: 0.2240
  time to fit residues: 54.5967
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  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  115 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 69 optimal weight:    0.2980
   chunk 50 optimal weight:    0.5980
   chunk 54 optimal weight:    0.1980
   chunk 47 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.112002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.099428 restraints weight = 9712.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.39
r_work: 0.3107 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6410  Z= 0.215
  Angle     :  0.519   8.840   8714  Z= 0.275
  Chirality :  0.040   0.148    977
  Planarity :  0.004   0.051   1092
  Dihedral  : 10.607  72.378    950
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.49 %
    Favored  : 79.91 %
  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:  0.34 (0.31), residues: 766
  helix:  1.51 (0.31), residues: 301
  sheet:  0.06 (0.48), residues: 127
  loop : -0.87 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.011   0.001   TYR A 426 
 ARG   0.006   0.000   ARG A 369 

*********************** 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
  214 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.8307 (tt) cc_final: 0.8060 (tp)
REVERT: A   84 GLN cc_start: 0.8049 (tt0) cc_final: 0.7593 (tt0)
REVERT: A   88 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7136 (mm-30)
REVERT: A  145 LYS cc_start: 0.8422 (ptmt) cc_final: 0.8071 (ptmt)
REVERT: A  166 CYS cc_start: 0.8098 (t) cc_final: 0.7740 (t)
REVERT: A  207 LEU cc_start: 0.8770 (pt) cc_final: 0.8504 (pp)
REVERT: A  231 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8391 (ttmm)
REVERT: A  280 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7458 (mt-10)
REVERT: A  425 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8244 (mttm)
REVERT: A  474 ASP cc_start: 0.8288 (m-30) cc_final: 0.8078 (m-30)
REVERT: A  510 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7904 (p)
REVERT: A  579 ARG cc_start: 0.7368 (mmp-170) cc_final: 0.7109 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8076 (mm)
REVERT: B   11 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7663 (pm20)
  outliers start: 24
  outliers final: 16
  residues processed: 197
  average time/residue: 0.2295
  time to fit residues: 56.5068
Evaluate side-chains
  209 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 189
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  382 HIS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  118 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.109899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.097552 restraints weight = 9682.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.37
r_work: 0.3091 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6410  Z= 0.339
  Angle     :  0.581   9.287   8714  Z= 0.309
  Chirality :  0.043   0.164    977
  Planarity :  0.004   0.051   1092
  Dihedral  : 10.677  76.012    950
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.64 %
    Favored  : 79.31 %
  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:  0.19 (0.31), residues: 766
  helix:  1.45 (0.31), residues: 301
  sheet: -0.18 (0.46), residues: 134
  loop : -0.96 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.004   0.001   HIS A  29 
 PHE   0.015   0.002   PHE B  52 
 TYR   0.016   0.002   TYR A 426 
 ARG   0.006   0.000   ARG A 369 

*********************** 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
  226 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.8132 (tt0) cc_final: 0.7663 (tt0)
REVERT: A  145 LYS cc_start: 0.8420 (ptmt) cc_final: 0.8076 (ptmt)
REVERT: A  166 CYS cc_start: 0.8232 (t) cc_final: 0.7896 (t)
REVERT: A  207 LEU cc_start: 0.8782 (pt) cc_final: 0.8548 (pp)
REVERT: A  231 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8492 (ttmm)
REVERT: A  280 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7545 (mt-10)
REVERT: A  404 ASP cc_start: 0.8356 (t0) cc_final: 0.8145 (t0)
REVERT: A  465 GLU cc_start: 0.8192 (tp30) cc_final: 0.7989 (tp30)
REVERT: A  474 ASP cc_start: 0.8321 (m-30) cc_final: 0.7982 (m-30)
REVERT: A  510 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7949 (p)
REVERT: A  579 ARG cc_start: 0.7494 (mmp-170) cc_final: 0.7232 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8121 (mm)
REVERT: B   11 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7703 (pm20)
  outliers start: 27
  outliers final: 18
  residues processed: 206
  average time/residue: 0.2389
  time to fit residues: 60.8648
Evaluate side-chains
  218 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 196
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  382 HIS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  605 GLU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  158 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 51 optimal weight:    0.2980
   chunk 25 optimal weight:    0.0980
   chunk 71 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3428 r_free = 0.3428 target = 0.111516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.098956 restraints weight = 9646.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.39
r_work: 0.3075 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6410  Z= 0.206
  Angle     :  0.545   9.403   8714  Z= 0.289
  Chirality :  0.041   0.135    977
  Planarity :  0.004   0.051   1092
  Dihedral  : 10.693  74.343    950
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.14 %
    Favored  : 78.41 %
  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:  0.20 (0.31), residues: 766
  helix:  1.49 (0.31), residues: 299
  sheet: -0.15 (0.46), residues: 132
  loop : -0.98 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.009   0.001   PHE A 127 
 TYR   0.010   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 369 

*********************** 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
  215 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6949 (m) cc_final: 0.6196 (p)
REVERT: A  145 LYS cc_start: 0.8441 (ptmt) cc_final: 0.8113 (ptmt)
REVERT: A  166 CYS cc_start: 0.8146 (t) cc_final: 0.7775 (t)
REVERT: A  207 LEU cc_start: 0.8732 (pt) cc_final: 0.8493 (pp)
REVERT: A  231 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8450 (ttmm)
REVERT: A  274 LEU cc_start: 0.8647 (tp) cc_final: 0.8419 (tt)
REVERT: A  280 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: A  425 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8207 (mttm)
REVERT: A  465 GLU cc_start: 0.8221 (tp30) cc_final: 0.7987 (tp30)
REVERT: A  474 ASP cc_start: 0.8283 (m-30) cc_final: 0.7942 (m-30)
REVERT: A  510 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7900 (p)
REVERT: A  552 ASP cc_start: 0.7783 (t0) cc_final: 0.7487 (t0)
REVERT: A  579 ARG cc_start: 0.7398 (mmp-170) cc_final: 0.7128 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8094 (mm)
REVERT: B   11 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7691 (pm20)
  outliers start: 23
  outliers final: 17
  residues processed: 198
  average time/residue: 0.2312
  time to fit residues: 57.1395
Evaluate side-chains
  210 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 189
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  158 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.1980
   chunk 72 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 75 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3430 r_free = 0.3430 target = 0.111565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.098893 restraints weight = 9811.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.43
r_work: 0.3081 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6410  Z= 0.214
  Angle     :  0.546   9.607   8714  Z= 0.289
  Chirality :  0.040   0.135    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 10.705  69.381    950
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.59 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.23 (0.31), residues: 766
  helix:  1.55 (0.31), residues: 300
  sheet: -0.16 (0.46), residues: 132
  loop : -1.00 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.011   0.001   TYR A 426 
 ARG   0.003   0.000   ARG A 369 

*********************** 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
  224 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 201
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.7020 (m) cc_final: 0.6350 (p)
REVERT: A   84 GLN cc_start: 0.8106 (tt0) cc_final: 0.7624 (tt0)
REVERT: A  145 LYS cc_start: 0.8438 (ptmt) cc_final: 0.8155 (ptmt)
REVERT: A  166 CYS cc_start: 0.8170 (t) cc_final: 0.7797 (t)
REVERT: A  207 LEU cc_start: 0.8750 (pt) cc_final: 0.8465 (pp)
REVERT: A  231 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8474 (ttmm)
REVERT: A  244 GLN cc_start: 0.8632 (pt0) cc_final: 0.8264 (pt0)
REVERT: A  274 LEU cc_start: 0.8648 (tp) cc_final: 0.8409 (tt)
REVERT: A  280 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7552 (mt-10)
REVERT: A  326 GLU cc_start: 0.8383 (tp30) cc_final: 0.7988 (tp30)
REVERT: A  386 ASP cc_start: 0.7628 (m-30) cc_final: 0.7408 (m-30)
REVERT: A  425 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8220 (mttm)
REVERT: A  465 GLU cc_start: 0.8249 (tp30) cc_final: 0.8036 (tp30)
REVERT: A  474 ASP cc_start: 0.8288 (m-30) cc_final: 0.7957 (m-30)
REVERT: A  510 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7902 (p)
REVERT: A  567 GLN cc_start: 0.7827 (tp40) cc_final: 0.7401 (tp40)
REVERT: A  579 ARG cc_start: 0.7400 (mmp-170) cc_final: 0.7120 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8089 (mm)
REVERT: B   11 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7709 (pm20)
  outliers start: 23
  outliers final: 18
  residues processed: 207
  average time/residue: 0.2344
  time to fit residues: 60.2084
Evaluate side-chains
  213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 191
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  260 ASP
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  158 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 31 optimal weight:    0.0770
   chunk 21 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 15 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0040
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.2950

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.112651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.099802 restraints weight = 9874.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.47
r_work: 0.3095 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6410  Z= 0.177
  Angle     :  0.538   9.633   8714  Z= 0.285
  Chirality :  0.040   0.133    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 10.662  71.040    950
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.34 %
    Favored  : 77.51 %
  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:  0.26 (0.31), residues: 766
  helix:  1.58 (0.31), residues: 300
  sheet: -0.03 (0.48), residues: 122
  loop : -1.03 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.003   0.000   HIS A 229 
 PHE   0.009   0.001   PHE A 127 
 TYR   0.010   0.001   TYR A 411 
 ARG   0.003   0.000   ARG A 369 

********************** 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
  218 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.7872 (tt0) cc_final: 0.7366 (tt0)
REVERT: A   88 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7050 (mm-30)
REVERT: A  137 MET cc_start: 0.8249 (mtp) cc_final: 0.8027 (mtp)
REVERT: A  166 CYS cc_start: 0.7937 (t) cc_final: 0.7535 (t)
REVERT: A  207 LEU cc_start: 0.8732 (pt) cc_final: 0.8454 (pp)
REVERT: A  231 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8303 (ttmm)
REVERT: A  244 GLN cc_start: 0.8385 (pt0) cc_final: 0.8022 (pt0)
REVERT: A  274 LEU cc_start: 0.8571 (tp) cc_final: 0.8329 (tt)
REVERT: A  420 VAL cc_start: 0.7918 (t) cc_final: 0.7691 (t)
REVERT: A  425 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8137 (mttm)
REVERT: A  474 ASP cc_start: 0.8079 (m-30) cc_final: 0.7746 (m-30)
REVERT: A  510 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7843 (p)
REVERT: A  579 ARG cc_start: 0.7147 (mmp-170) cc_final: 0.6866 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7992 (mm)
REVERT: B   11 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7553 (pm20)
  outliers start: 21
  outliers final: 16
  residues processed: 203
  average time/residue: 0.2174
  time to fit residues: 55.3252
Evaluate side-chains
  211 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 191
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  470 CYS
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  150 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0040
   chunk 64 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 4 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.4192

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.112020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.099217 restraints weight = 9923.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.47
r_work: 0.3117 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6410  Z= 0.212
  Angle     :  0.555   9.627   8714  Z= 0.293
  Chirality :  0.040   0.136    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 10.663  72.725    950
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.59 %
    Favored  : 77.81 %
  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:  0.28 (0.31), residues: 766
  helix:  1.61 (0.31), residues: 300
  sheet: -0.13 (0.46), residues: 132
  loop : -0.99 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.014   0.001   PHE A  52 
 TYR   0.014   0.001   TYR B 113 
 ARG   0.007   0.000   ARG A  51 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3337.06 seconds
wall clock time: 60 minutes 4.23 seconds (3604.23 seconds total)