Starting phenix.real_space_refine
on Thu Nov 14 12:31:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca1_45379/11_2024/9ca1_45379_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca1_45379/11_2024/9ca1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca1_45379/11_2024/9ca1_45379.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca1_45379/11_2024/9ca1_45379.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca1_45379/11_2024/9ca1_45379_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ca1_45379/11_2024/9ca1_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.99, per 1000 atoms: 0.80
  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: 1.67
  Conformation dependent library (CDL) restraints added in 906.6 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: 2.06
  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: 1.86

  Time building geometry restraints manager: 1.91 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:             2.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.470
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.540
-------------------------------------------------------------------------------
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  : 0.712 
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: 0.2297
  time to fit residues: 61.2770
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  : 0.675 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
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  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.7369 (tt0) cc_final: 0.7002 (tt0)
REVERT: A  145 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7560 (ptmt)
REVERT: A  166 CYS cc_start: 0.7429 (t) cc_final: 0.7117 (t)
REVERT: A  274 LEU cc_start: 0.8574 (tp) cc_final: 0.8331 (tt)
REVERT: A  425 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7954 (mttp)
REVERT: A  510 THR cc_start: 0.8154 (m) cc_final: 0.7782 (p)
REVERT: A  579 ARG cc_start: 0.6940 (mmp-170) cc_final: 0.6708 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8354 (mm) cc_final: 0.7981 (mm)
  outliers start: 11
  outliers final: 8
  residues processed: 200
  average time/residue: 0.2321
  time to fit residues: 57.7521
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  : 0.725 
-------------------------------------------------------------------------------
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 38 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0000
   chunk 19 optimal weight:    0.3980
   chunk 70 optimal weight:    0.0980
   chunk 75 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0470
   chunk 23 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.2482

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6410  Z= 0.159
  Angle     :  0.508   7.828   8714  Z= 0.270
  Chirality :  0.039   0.137    977
  Planarity :  0.004   0.054   1092
  Dihedral  : 10.758  76.154    950
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.26 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.34 %
    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:  0.37 (0.31), residues: 766
  helix:  1.48 (0.31), residues: 301
  sheet:  0.21 (0.48), residues: 122
  loop : -0.84 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 458 
 HIS   0.003   0.000   HIS A 229 
 PHE   0.011   0.001   PHE A 214 
 TYR   0.010   0.001   TYR A 411 
 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
  211 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 196
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6220 (m) cc_final: 0.5429 (p)
REVERT: A   84 GLN cc_start: 0.7328 (tt0) cc_final: 0.6832 (tt0)
REVERT: A  145 LYS cc_start: 0.8134 (ptmt) cc_final: 0.7667 (ptmt)
REVERT: A  166 CYS cc_start: 0.7385 (t) cc_final: 0.6979 (t)
REVERT: A  231 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8027 (tttp)
REVERT: A  274 LEU cc_start: 0.8526 (tp) cc_final: 0.8286 (tt)
REVERT: A  425 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7881 (mttm)
REVERT: A  510 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7825 (p)
REVERT: A  552 ASP cc_start: 0.7341 (t0) cc_final: 0.7070 (t0)
REVERT: A  579 ARG cc_start: 0.6881 (mmp-170) cc_final: 0.6626 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7894 (mm)
REVERT: B   11 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7344 (pm20)
  outliers start: 15
  outliers final: 8
  residues processed: 199
  average time/residue: 0.2300
  time to fit residues: 56.9669
Evaluate side-chains
  199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 187
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
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   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  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 69 optimal weight:    0.0980
   chunk 52 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0070
   chunk 70 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.4598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1215

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= 0.216
  Angle     :  0.515   8.230   8714  Z= 0.274
  Chirality :  0.040   0.135    977
  Planarity :  0.004   0.053   1092
  Dihedral  : 10.717  74.939    950
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.26 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.74 %
    Favored  : 82.46 %
  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:  0.40 (0.31), residues: 766
  helix:  1.53 (0.31), residues: 301
  sheet:  0.13 (0.47), residues: 127
  loop : -0.83 (0.33), 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   0.012   0.001   PHE A 127 
 TYR   0.012   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
  203 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 191
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6364 (m) cc_final: 0.5604 (p)
REVERT: A   63 THR cc_start: 0.8085 (t) cc_final: 0.7835 (m)
REVERT: A   84 GLN cc_start: 0.7384 (tt0) cc_final: 0.6984 (tt0)
REVERT: A  145 LYS cc_start: 0.8148 (ptmt) cc_final: 0.7688 (ptmt)
REVERT: A  166 CYS cc_start: 0.7415 (t) cc_final: 0.7054 (t)
REVERT: A  231 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8038 (tttp)
REVERT: A  425 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7930 (mttm)
REVERT: A  510 THR cc_start: 0.8189 (m) cc_final: 0.7826 (p)
REVERT: A  567 GLN cc_start: 0.7541 (tp40) cc_final: 0.6993 (tp40)
REVERT: A  579 ARG cc_start: 0.6888 (mmp-170) cc_final: 0.6628 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7884 (mm)
REVERT: B   11 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7371 (pm20)
REVERT: B   94 MET cc_start: 0.8136 (ttm) cc_final: 0.7917 (ttt)
  outliers start: 12
  outliers final: 7
  residues processed: 193
  average time/residue: 0.2272
  time to fit residues: 54.8674
Evaluate side-chains
  197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 187
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0570
   chunk 66 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.7100

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   6410  Z= 0.296
  Angle     :  0.545   8.688   8714  Z= 0.288
  Chirality :  0.042   0.138    977
  Planarity :  0.004   0.052   1092
  Dihedral  : 10.790  74.983    950
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.44 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.94 %
    Favored  : 80.06 %
  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:  1.46 (0.31), residues: 302
  sheet:  0.07 (0.47), residues: 127
  loop : -0.88 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.004   0.001   HIS A  29 
 PHE   0.012   0.002   PHE A 127 
 TYR   0.014   0.001   TYR A 426 
 ARG   0.004   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
  210 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6529 (m) cc_final: 0.5708 (p)
REVERT: A   84 GLN cc_start: 0.7410 (tt0) cc_final: 0.6955 (tt0)
REVERT: A  145 LYS cc_start: 0.8186 (ptmt) cc_final: 0.7727 (ptmt)
REVERT: A  166 CYS cc_start: 0.7463 (t) cc_final: 0.7146 (t)
REVERT: A  231 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7928 (ttmm)
REVERT: A  425 LYS cc_start: 0.8319 (mtmm) cc_final: 0.7945 (mttm)
REVERT: A  510 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7900 (p)
REVERT: A  579 ARG cc_start: 0.6932 (mmp-170) cc_final: 0.6673 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7879 (mm)
REVERT: B   11 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7421 (pm20)
REVERT: B   94 MET cc_start: 0.8149 (ttm) cc_final: 0.7898 (ttt)
  outliers start: 20
  outliers final: 14
  residues processed: 196
  average time/residue: 0.2290
  time to fit residues: 56.2309
Evaluate side-chains
  209 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  274 LEU
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
Chi-restraints excluded: chain B residue  118 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 67 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.5378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6410  Z= 0.237
  Angle     :  0.535   8.864   8714  Z= 0.282
  Chirality :  0.041   0.136    977
  Planarity :  0.004   0.052   1092
  Dihedral  : 10.738  74.248    950
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  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:  0.24 (0.31), residues: 766
  helix:  1.46 (0.31), residues: 301
  sheet: -0.09 (0.46), residues: 132
  loop : -0.92 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 422 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.012   0.001   TYR A 426 
 ARG   0.002   0.000   ARG A 591 

*********************** 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
  213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 190
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6499 (m) cc_final: 0.5684 (p)
REVERT: A   84 GLN cc_start: 0.7388 (tt0) cc_final: 0.6916 (tt0)
REVERT: A   88 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6587 (mm-30)
REVERT: A  145 LYS cc_start: 0.8151 (ptmt) cc_final: 0.7764 (ptmt)
REVERT: A  166 CYS cc_start: 0.7467 (t) cc_final: 0.7132 (t)
REVERT: A  231 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7928 (ttmm)
REVERT: A  425 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7940 (mttm)
REVERT: A  510 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7880 (p)
REVERT: A  579 ARG cc_start: 0.6913 (mmp-170) cc_final: 0.6644 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7851 (mm)
REVERT: B   11 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7386 (pm20)
REVERT: B   94 MET cc_start: 0.8154 (ttm) cc_final: 0.7894 (ttt)
  outliers start: 23
  outliers final: 16
  residues processed: 198
  average time/residue: 0.2284
  time to fit residues: 56.2850
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  : 0.732 
-------------------------------------------------------------------------------
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  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  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  142 LEU
Chi-restraints excluded: chain B residue  158 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0980
   chunk 62 optimal weight:    0.0870
   chunk 41 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6410  Z= 0.245
  Angle     :  0.546   9.137   8714  Z= 0.287
  Chirality :  0.041   0.156    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 10.685  74.523    950
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.44 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.09 %
    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:  0.21 (0.31), residues: 766
  helix:  1.42 (0.31), residues: 301
  sheet: -0.09 (0.46), residues: 132
  loop : -0.94 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A 422 
 PHE   0.013   0.002   PHE B  52 
 TYR   0.012   0.001   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
  223 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 193
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6568 (m) cc_final: 0.5744 (p)
REVERT: A   84 GLN cc_start: 0.7400 (tt0) cc_final: 0.6941 (tt0)
REVERT: A  145 LYS cc_start: 0.8144 (ptmt) cc_final: 0.7731 (ptmt)
REVERT: A  166 CYS cc_start: 0.7445 (t) cc_final: 0.7131 (t)
REVERT: A  231 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7930 (ttmm)
REVERT: A  280 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7080 (mt-10)
REVERT: A  404 ASP cc_start: 0.7924 (t0) cc_final: 0.7684 (t0)
REVERT: A  425 LYS cc_start: 0.8321 (mtmm) cc_final: 0.7947 (mttm)
REVERT: A  510 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7887 (p)
REVERT: A  579 ARG cc_start: 0.6884 (mmp-170) cc_final: 0.6599 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7859 (mm)
REVERT: B   11 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7396 (pm20)
  outliers start: 30
  outliers final: 19
  residues processed: 203
  average time/residue: 0.2127
  time to fit residues: 54.0585
Evaluate side-chains
  223 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 200
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
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  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  142 LEU
Chi-restraints excluded: chain B residue  150 LEU
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 22 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 36 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 67 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0060
   overall best weight:    0.3596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6410  Z= 0.191
  Angle     :  0.539   9.253   8714  Z= 0.283
  Chirality :  0.040   0.148    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 10.652  73.495    950
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.74 %
    Favored  : 78.11 %
  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:  0.24 (0.31), residues: 766
  helix:  1.47 (0.31), residues: 301
  sheet: -0.01 (0.47), residues: 127
  loop : -0.97 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 115 
 HIS   0.003   0.000   HIS A 229 
 PHE   0.010   0.001   PHE A 127 
 TYR   0.010   0.001   TYR A 411 
 ARG   0.003   0.000   ARG A 591 

*********************** 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
  224 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6502 (m) cc_final: 0.5878 (p)
REVERT: A   84 GLN cc_start: 0.7374 (tt0) cc_final: 0.6921 (tt0)
REVERT: A  145 LYS cc_start: 0.8202 (ptmt) cc_final: 0.7834 (ptmt)
REVERT: A  166 CYS cc_start: 0.7442 (t) cc_final: 0.7080 (t)
REVERT: A  231 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7881 (ttmm)
REVERT: A  280 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7109 (mt-10)
REVERT: A  386 ASP cc_start: 0.7142 (m-30) cc_final: 0.6928 (m-30)
REVERT: A  404 ASP cc_start: 0.7955 (t0) cc_final: 0.7706 (t0)
REVERT: A  425 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7928 (mttm)
REVERT: A  510 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7853 (p)
REVERT: A  579 ARG cc_start: 0.6877 (mmp-170) cc_final: 0.6589 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7844 (mm)
REVERT: B   11 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7368 (pm20)
  outliers start: 21
  outliers final: 16
  residues processed: 209
  average time/residue: 0.2300
  time to fit residues: 60.7632
Evaluate side-chains
  213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 193
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  115 SER
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  150 LEU
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 71 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    0.3980
   chunk 21 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.4778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1589

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= 0.227
  Angle     :  0.562   9.503   8714  Z= 0.295
  Chirality :  0.041   0.145    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 10.700  69.615    950
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  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:  0.26 (0.31), residues: 766
  helix:  1.51 (0.31), residues: 301
  sheet: -0.07 (0.46), residues: 132
  loop : -0.97 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.002   0.001   HIS A 422 
 PHE   0.012   0.001   PHE A 127 
 TYR   0.011   0.001   TYR A 426 
 ARG   0.004   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
  217 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 193
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6764 (m) cc_final: 0.6065 (p)
REVERT: A   84 GLN cc_start: 0.7423 (tt0) cc_final: 0.6981 (tt0)
REVERT: A  145 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7883 (ptmt)
REVERT: A  166 CYS cc_start: 0.7465 (t) cc_final: 0.7104 (t)
REVERT: A  231 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7870 (ttmm)
REVERT: A  244 GLN cc_start: 0.8089 (pt0) cc_final: 0.7672 (pt0)
REVERT: A  404 ASP cc_start: 0.7988 (t0) cc_final: 0.7686 (t70)
REVERT: A  425 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7944 (mttm)
REVERT: A  510 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7876 (p)
REVERT: A  567 GLN cc_start: 0.7548 (tp40) cc_final: 0.7001 (tp40)
REVERT: A  579 ARG cc_start: 0.6894 (mmp-170) cc_final: 0.6603 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7854 (mm)
REVERT: B   11 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7388 (pm20)
  outliers start: 24
  outliers final: 18
  residues processed: 202
  average time/residue: 0.2243
  time to fit residues: 56.5150
Evaluate side-chains
  215 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 193
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  142 LEU
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 34 optimal weight:    0.9980
   chunk 50 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0170
   chunk 37 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.5418

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6410  Z= 0.246
  Angle     :  0.580   9.615   8714  Z= 0.303
  Chirality :  0.041   0.143    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 10.722  71.400    950
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.59 %
    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:  0.20 (0.31), residues: 766
  helix:  1.50 (0.31), residues: 300
  sheet: -0.22 (0.46), residues: 134
  loop : -0.97 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.003   0.001   HIS A  29 
 PHE   0.013   0.001   PHE A  52 
 TYR   0.012   0.001   TYR A 426 
 ARG   0.007   0.000   ARG A  51 

********************** 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: 26
    poor density    : 192
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 SER cc_start: 0.6777 (m) cc_final: 0.6098 (p)
REVERT: A   84 GLN cc_start: 0.7444 (tt0) cc_final: 0.6970 (tt0)
REVERT: A  137 MET cc_start: 0.7986 (mtp) cc_final: 0.7781 (mtp)
REVERT: A  145 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7905 (ptmt)
REVERT: A  166 CYS cc_start: 0.7500 (t) cc_final: 0.7169 (t)
REVERT: A  231 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7871 (ttmm)
REVERT: A  244 GLN cc_start: 0.8078 (pt0) cc_final: 0.7667 (pt0)
REVERT: A  425 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7931 (mttm)
REVERT: A  510 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7830 (p)
REVERT: A  567 GLN cc_start: 0.7573 (tp40) cc_final: 0.7121 (tp40)
REVERT: A  579 ARG cc_start: 0.6912 (mmp-170) cc_final: 0.6618 (mmp-170)
REVERT: B    9 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7863 (mm)
REVERT: B   11 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7403 (pm20)
  outliers start: 26
  outliers final: 20
  residues processed: 203
  average time/residue: 0.2291
  time to fit residues: 58.0519
Evaluate side-chains
  215 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue  116 LEU
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  142 LEU
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 56 optimal weight:    0.2980
   chunk 9 optimal weight:    0.0970
   chunk 16 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 62 optimal weight:    0.3980
   chunk 7 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 = 0.112409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.099675 restraints weight = 9640.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.44
r_work: 0.3085 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1665

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= 0.194
  Angle     :  0.559   9.550   8714  Z= 0.292
  Chirality :  0.040   0.141    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 10.703  71.913    950
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.44 %
    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:  0.26 (0.31), residues: 766
  helix:  1.56 (0.31), residues: 300
  sheet: -0.13 (0.46), residues: 132
  loop : -0.97 (0.32), residues: 334

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   0.012   0.001   PHE A  52 
 TYR   0.010   0.001   TYR A 411 
 ARG   0.003   0.000   ARG A 369 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2041.65 seconds
wall clock time: 48 minutes 32.51 seconds (2912.51 seconds total)