Starting phenix.real_space_refine
on Wed Mar 12 11:46:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wu2_32817/03_2025/7wu2_32817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wu2_32817/03_2025/7wu2_32817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wu2_32817/03_2025/7wu2_32817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wu2_32817/03_2025/7wu2_32817.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wu2_32817/03_2025/7wu2_32817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wu2_32817/03_2025/7wu2_32817.cif"
  }
  resolution = 2.8
  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=   0.000 sd=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4968      2.51       5
     N    1361      2.21       5
     O    1450      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7829
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1734
          Classifications: {'peptide': 210}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2586
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 423
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2115
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 7, 'TRANS': 269}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 22
  Time building chain proxies: 5.18, per 1000 atoms: 0.66
  Number of scatterers: 7829
  At special positions: 0
  Unit cell: (106.029, 118.881, 83.538, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1450      8.00
     N    1361      7.00
     C    4968      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 632 " - pdb=" SG  CYS R 704 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1892

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      40.5% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 40
    Processing helix  chain 'A' and resid 53 through 57
      removed outlier: 3.904A  pdb=" N   VAL A  57 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.675A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.520A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.196A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.860A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.613A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.733A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 25
      removed outlier: 4.305A  pdb=" N   ILE C  25 " --> pdb=" O   MET C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.532A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.606A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.503A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 559 through 591
    Processing helix  chain 'R' and resid 592 through 594
      No H-bonds generated for 'chain 'R' and resid 592 through 594'
    Processing helix  chain 'R' and resid 601 through 623
    Processing helix  chain 'R' and resid 629 through 662
      removed outlier: 4.006A  pdb=" N   VAL R 637 " --> pdb=" O   GLN R 633 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA R 646 " --> pdb=" O   PHE R 642 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 671 through 680
    Processing helix  chain 'R' and resid 680 through 694
      removed outlier: 3.706A  pdb=" N   LEU R 684 " --> pdb=" O   TRP R 680 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE R 693 " --> pdb=" O   ILE R 689 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 713 through 737
      Proline residue:  R 719  - end of helix
    Processing helix  chain 'R' and resid 738 through 745
    Processing helix  chain 'R' and resid 745 through 750
      removed outlier: 4.002A  pdb=" N   HIS R 749 " --> pdb=" O   ASN R 745 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 752 through 764
      removed outlier: 3.967A  pdb=" N   LYS R 756 " --> pdb=" O   PRO R 752 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU R 757 " --> pdb=" O   SER R 753 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   THR R 758 " --> pdb=" O   ALA R 754 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 764 through 770
      removed outlier: 4.572A  pdb=" N   ILE R 768 " --> pdb=" O   VAL R 764 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 773 through 778
      removed outlier: 3.822A  pdb=" N   VAL R 777 " --> pdb=" O   TRP R 773 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 779 through 781
      No H-bonds generated for 'chain 'R' and resid 779 through 781'
    Processing helix  chain 'R' and resid 783 through 797
      removed outlier: 3.647A  pdb=" N   PHE R 787 " --> pdb=" O   CYS R 783 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 797 through 807
    Processing helix  chain 'R' and resid 810 through 821
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 6.251A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.759A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.714A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 6.393A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.556A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.047A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.448A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.046A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.017A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    384 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 3.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2552
        1.34 -     1.46: 1364
        1.46 -     1.58: 4006
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 7992
  Sorted by residual:
  bond pdb=" N   ARG A 265 "
       pdb=" CA  ARG A 265 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.35e-02 5.49e+03 5.23e+00
  bond pdb=" N   ASN A 254 "
       pdb=" CA  ASN A 254 "
    ideal  model  delta    sigma   weight residual
    1.460  1.487 -0.027 1.22e-02 6.72e+03 5.05e+00
  bond pdb=" N   TYR A 253 "
       pdb=" CA  TYR A 253 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.42e-02 4.96e+03 4.84e+00
  bond pdb=" N   ASN A  50 "
       pdb=" CA  ASN A  50 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 1.03e+00
  bond pdb=" CA  ASN A  50 "
       pdb=" CB  ASN A  50 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.69e-02 3.50e+03 1.02e+00
  ... (remaining 7987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 10714
        1.89 -     3.78: 109
        3.78 -     5.66: 16
        5.66 -     7.55: 3
        7.55 -     9.44: 3
  Bond angle restraints: 10845
  Sorted by residual:
  angle pdb=" C   ASP A  49 "
        pdb=" N   ASN A  50 "
        pdb=" CA  ASN A  50 "
      ideal   model   delta    sigma   weight residual
     121.54  130.98   -9.44 1.91e+00 2.74e-01 2.44e+01
  angle pdb=" CB  ARG B   8 "
        pdb=" CG  ARG B   8 "
        pdb=" CD  ARG B   8 "
      ideal   model   delta    sigma   weight residual
     111.30  119.21   -7.91 2.30e+00 1.89e-01 1.18e+01
  angle pdb=" C   ASN R 546 "
        pdb=" N   PHE R 547 "
        pdb=" CA  PHE R 547 "
      ideal   model   delta    sigma   weight residual
     121.54  127.92   -6.38 1.91e+00 2.74e-01 1.12e+01
  angle pdb=" N   GLU A 299 "
        pdb=" CA  GLU A 299 "
        pdb=" CB  GLU A 299 "
      ideal   model   delta    sigma   weight residual
     110.28  114.62   -4.34 1.55e+00 4.16e-01 7.84e+00
  angle pdb=" N   ASN A  50 "
        pdb=" CA  ASN A  50 "
        pdb=" CB  ASN A  50 "
      ideal   model   delta    sigma   weight residual
     110.49  115.04   -4.55 1.69e+00 3.50e-01 7.25e+00
  ... (remaining 10840 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4345
       17.88 -    35.75: 321
       35.75 -    53.63: 47
       53.63 -    71.51: 9
       71.51 -    89.38: 7
  Dihedral angle restraints: 4729
    sinusoidal: 1800
      harmonic: 2929
  Sorted by residual:
  dihedral pdb=" CB  CYS R 632 "
           pdb=" SG  CYS R 632 "
           pdb=" SG  CYS R 704 "
           pdb=" CB  CYS R 704 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -132.06   46.06     1      1.00e+01 1.00e-02 2.94e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -42.57  -43.43     1      1.00e+01 1.00e-02 2.63e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.12  -19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 4726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 876
       0.037 -    0.075: 263
       0.075 -    0.112: 73
       0.112 -    0.149: 22
       0.149 -    0.186: 2
  Chirality restraints: 1236
  Sorted by residual:
  chirality pdb=" CA  ASN A  50 "
            pdb=" N   ASN A  50 "
            pdb=" C   ASN A  50 "
            pdb=" CB  ASN A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.68e-01
  chirality pdb=" CB  VAL N 110 "
            pdb=" CA  VAL N 110 "
            pdb=" CG1 VAL N 110 "
            pdb=" CG2 VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.18e-01
  chirality pdb=" CA  THR R 630 "
            pdb=" N   THR R 630 "
            pdb=" C   THR R 630 "
            pdb=" CB  THR R 630 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 1233 not shown)

  Planarity restraints: 1385
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  49 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.94e+00
        pdb=" C   ASP A  49 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASP A  49 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A  50 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 252 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   ASP A 252 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASP A 252 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TYR A 253 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 598 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.95e+00
        pdb=" C   ARG R 598 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ARG R 598 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASN R 599 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1382 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 516
        2.74 -     3.28: 7936
        3.28 -     3.82: 13282
        3.82 -     4.36: 15829
        4.36 -     4.90: 27202
  Nonbonded interactions: 64765
  Sorted by model distance:
  nonbonded pdb=" O   THR R 596 "
            pdb=" ND2 ASN R 599 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   ASP R 696 "
            pdb=" OG1 THR R 700 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" NE2 GLN B 220 "
            pdb=" OD1 ASP B 258 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.314 3.040
  ... (remaining 64760 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:             1.030
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.010
  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:             0.010
  Load rotamer database and sin/cos tables:15.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7992  Z= 0.130
  Angle     :  0.513   9.441  10845  Z= 0.275
  Chirality :  0.041   0.186   1236
  Planarity :  0.003   0.040   1385
  Dihedral  : 12.858  89.384   2828
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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:  0.79 (0.27), residues: 998
  helix:  1.38 (0.29), residues: 369
  sheet:  0.65 (0.34), residues: 224
  loop : -0.27 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.009   0.001   HIS B 266 
 PHE   0.010   0.001   PHE N  29 
 TYR   0.013   0.001   TYR R 789 
 ARG   0.009   0.000   ARG B   8 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A   55 THR cc_start: 0.7759 (m) cc_final: 0.7467 (p)
REVERT: A  307 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7655 (mmmt)
REVERT: A  343 ASP cc_start: 0.6462 (m-30) cc_final: 0.6038 (m-30)
REVERT: R  804 LEU cc_start: 0.8517 (tt) cc_final: 0.8243 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 1.2269
  time to fit residues: 202.5380
Evaluate side-chains
  122 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0670
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.2126

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

Flipped N/Q/H residues before XYZ refinement:
A 254 ASN
A 371 ASN
B  32 GLN
B 175 GLN
B 266 HIS
N  31 ASN
R 562 HIS
R 600 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.168129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.132274 restraints weight = 8096.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 1.67
r_work: 0.3360 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7992  Z= 0.318
  Angle     :  0.632   8.490  10845  Z= 0.336
  Chirality :  0.045   0.148   1236
  Planarity :  0.004   0.044   1385
  Dihedral  :  4.567  30.029   1095
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  :  9.67 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.96 (0.27), residues: 998
  helix:  1.82 (0.28), residues: 356
  sheet:  0.41 (0.34), residues: 216
  loop : -0.18 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 339 
 HIS   0.013   0.002   HIS A 357 
 PHE   0.018   0.002   PHE R 665 
 TYR   0.025   0.002   TYR B  59 
 ARG   0.006   0.001   ARG B   8 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.6945 (mtt180)
REVERT: B  156 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8571 (pt0)
REVERT: N   31 ASN cc_start: 0.8424 (m-40) cc_final: 0.8121 (m-40)
  outliers start: 32
  outliers final: 14
  residues processed: 135
  average time/residue: 1.1263
  time to fit residues: 162.9635
Evaluate side-chains
  122 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  586 VAL
Chi-restraints excluded: chain R residue  660 MET
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  771 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 57 optimal weight:    0.3980
   chunk 96 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0060
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.7998

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  75 GLN
B 175 GLN
B 266 HIS
R 562 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.168216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.131533 restraints weight = 8181.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.69
r_work: 0.3374 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7992  Z= 0.218
  Angle     :  0.532   8.650  10845  Z= 0.285
  Chirality :  0.042   0.168   1236
  Planarity :  0.003   0.041   1385
  Dihedral  :  4.308  31.366   1095
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.63 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.97 (0.27), residues: 998
  helix:  1.90 (0.28), residues: 364
  sheet:  0.44 (0.34), residues: 214
  loop : -0.31 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.004   0.000   ARG A 317 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7502 (p0)
REVERT: A  314 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7459 (mm-30)
REVERT: B  156 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8389 (pt0)
REVERT: N   43 LYS cc_start: 0.7397 (mtpp) cc_final: 0.6614 (mmtp)
REVERT: N   77 ASN cc_start: 0.7994 (m-40) cc_final: 0.7610 (m-40)
  outliers start: 31
  outliers final: 15
  residues processed: 123
  average time/residue: 1.3629
  time to fit residues: 178.2428
Evaluate side-chains
  119 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue  660 MET
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  777 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
B 266 HIS
R 562 HIS
R 600 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.167581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131753 restraints weight = 8165.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.61
r_work: 0.3361 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7992  Z= 0.242
  Angle     :  0.552  10.082  10845  Z= 0.295
  Chirality :  0.042   0.150   1236
  Planarity :  0.004   0.040   1385
  Dihedral  :  4.394  30.537   1095
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 16.47 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.83 (0.27), residues: 998
  helix:  1.85 (0.28), residues: 362
  sheet:  0.40 (0.34), residues: 214
  loop : -0.47 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.012   0.002   PHE B 199 
 TYR   0.014   0.001   TYR N  95 
 ARG   0.004   0.000   ARG A 317 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 106
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7339 (tt0)
REVERT: A  314 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7937 (mm-30)
REVERT: N   77 ASN cc_start: 0.7963 (m-40) cc_final: 0.7717 (m-40)
  outliers start: 37
  outliers final: 17
  residues processed: 126
  average time/residue: 1.1861
  time to fit residues: 159.0811
Evaluate side-chains
  115 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue  586 VAL
Chi-restraints excluded: chain R residue  660 MET
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  771 THR
Chi-restraints excluded: chain R residue  777 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 71 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0570
   chunk 55 optimal weight:    0.9980
   chunk 86 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 65 optimal weight:    0.4980
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R 562 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.167741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130728 restraints weight = 7995.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.76
r_work: 0.3341 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7992  Z= 0.201
  Angle     :  0.513   7.309  10845  Z= 0.276
  Chirality :  0.041   0.151   1236
  Planarity :  0.003   0.040   1385
  Dihedral  :  4.300  34.747   1095
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 17.90 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.86 (0.27), residues: 998
  helix:  1.95 (0.28), residues: 362
  sheet:  0.33 (0.33), residues: 214
  loop : -0.48 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.004   0.000   ARG A 317 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7405 (tt0)
REVERT: A  314 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7961 (mm-30)
REVERT: B  156 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8353 (pt0)
REVERT: N   43 LYS cc_start: 0.7658 (mtpp) cc_final: 0.6878 (mmtp)
REVERT: N   77 ASN cc_start: 0.7993 (m-40) cc_final: 0.7753 (m-40)
  outliers start: 30
  outliers final: 14
  residues processed: 119
  average time/residue: 1.0728
  time to fit residues: 136.4158
Evaluate side-chains
  112 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  777 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 175 GLN
R 562 HIS
R 600 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.163338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.126000 restraints weight = 8046.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.79
r_work: 0.3273 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7992  Z= 0.363
  Angle     :  0.623   9.545  10845  Z= 0.333
  Chirality :  0.045   0.170   1236
  Planarity :  0.004   0.040   1385
  Dihedral  :  4.756  37.508   1095
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.14 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.55 (0.26), residues: 998
  helix:  1.58 (0.27), residues: 362
  sheet:  0.32 (0.33), residues: 220
  loop : -0.65 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.013   0.002   PHE A 208 
 TYR   0.016   0.002   TYR N  95 
 ARG   0.004   0.001   ARG A 317 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7398 (tt0)
REVERT: A  314 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7538 (mm-30)
REVERT: B  156 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8397 (mt0)
REVERT: N   43 LYS cc_start: 0.7688 (mtpp) cc_final: 0.6905 (mmtp)
REVERT: R  735 THR cc_start: 0.7791 (m) cc_final: 0.7526 (p)
  outliers start: 36
  outliers final: 20
  residues processed: 118
  average time/residue: 1.1408
  time to fit residues: 143.7880
Evaluate side-chains
  116 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  586 VAL
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  766 LEU
Chi-restraints excluded: chain R residue  777 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 82 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.166121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.128922 restraints weight = 8091.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.78
r_work: 0.3303 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7992  Z= 0.224
  Angle     :  0.531   8.018  10845  Z= 0.286
  Chirality :  0.042   0.154   1236
  Planarity :  0.003   0.039   1385
  Dihedral  :  4.466  36.445   1095
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.97 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.72 (0.26), residues: 998
  helix:  1.79 (0.28), residues: 362
  sheet:  0.37 (0.34), residues: 212
  loop : -0.58 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.004   0.000   ARG A 317 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7394 (tt0)
REVERT: A  314 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8019 (mm-30)
REVERT: B  156 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8339 (pt0)
REVERT: B  171 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7839 (mm)
REVERT: N   43 LYS cc_start: 0.7682 (mtpp) cc_final: 0.6926 (mmtp)
REVERT: N   77 ASN cc_start: 0.7990 (m-40) cc_final: 0.7725 (m-40)
REVERT: R  735 THR cc_start: 0.7800 (m) cc_final: 0.7525 (p)
  outliers start: 31
  outliers final: 18
  residues processed: 123
  average time/residue: 1.1462
  time to fit residues: 150.5120
Evaluate side-chains
  118 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue  566 LEU
Chi-restraints excluded: chain R residue  586 VAL
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  766 LEU
Chi-restraints excluded: chain R residue  777 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 79 optimal weight:    0.3980
   chunk 80 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R 562 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.165481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.128278 restraints weight = 8151.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.77
r_work: 0.3289 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7992  Z= 0.292
  Angle     :  0.576   9.705  10845  Z= 0.309
  Chirality :  0.043   0.161   1236
  Planarity :  0.004   0.039   1385
  Dihedral  :  4.614  37.211   1095
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.69 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.64 (0.26), residues: 998
  helix:  1.69 (0.27), residues: 362
  sheet:  0.33 (0.33), residues: 218
  loop : -0.60 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.014   0.002   PHE B 199 
 TYR   0.014   0.002   TYR N  95 
 ARG   0.007   0.000   ARG A 317 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8436 (mmt180) cc_final: 0.8197 (mmt90)
REVERT: A  268 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7415 (tt0)
REVERT: A  314 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7580 (mm-30)
REVERT: N   43 LYS cc_start: 0.7696 (mtpp) cc_final: 0.6929 (mmtp)
REVERT: R  735 THR cc_start: 0.7833 (m) cc_final: 0.7557 (p)
  outliers start: 32
  outliers final: 21
  residues processed: 118
  average time/residue: 1.1762
  time to fit residues: 148.1991
Evaluate side-chains
  118 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue  566 LEU
Chi-restraints excluded: chain R residue  586 VAL
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  695 MET
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  766 LEU
Chi-restraints excluded: chain R residue  777 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 29 optimal weight:    0.0970
   chunk 91 optimal weight:    0.3980
   chunk 39 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 86 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 42 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R 562 HIS
R 600 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.169199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.132356 restraints weight = 8143.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.80
r_work: 0.3358 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7992  Z= 0.150
  Angle     :  0.487   7.658  10845  Z= 0.261
  Chirality :  0.040   0.145   1236
  Planarity :  0.003   0.040   1385
  Dihedral  :  4.179  34.928   1095
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.12 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.89 (0.27), residues: 998
  helix:  2.07 (0.28), residues: 362
  sheet:  0.29 (0.34), residues: 208
  loop : -0.51 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.008   0.001   TYR R 602 
 ARG   0.007   0.000   ARG A 317 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A   49 ASP cc_start: 0.6686 (p0) cc_final: 0.6447 (p0)
REVERT: A  268 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7369 (tt0)
REVERT: A  314 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8055 (mm-30)
REVERT: N   43 LYS cc_start: 0.7623 (mtpp) cc_final: 0.6873 (mmtp)
REVERT: N   77 ASN cc_start: 0.7993 (m-40) cc_final: 0.7749 (m-40)
REVERT: R  735 THR cc_start: 0.8028 (m) cc_final: 0.7768 (p)
  outliers start: 21
  outliers final: 12
  residues processed: 113
  average time/residue: 1.1653
  time to fit residues: 140.1978
Evaluate side-chains
  112 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain R residue  566 LEU
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  777 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 83 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R 562 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.164691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125166 restraints weight = 8073.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.90
r_work: 0.3283 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7992  Z= 0.260
  Angle     :  0.559   8.660  10845  Z= 0.297
  Chirality :  0.043   0.169   1236
  Planarity :  0.004   0.039   1385
  Dihedral  :  4.446  36.422   1095
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 22.20 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.80 (0.27), residues: 998
  helix:  1.90 (0.28), residues: 362
  sheet:  0.26 (0.33), residues: 219
  loop : -0.51 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.012   0.002   PHE B 199 
 TYR   0.013   0.002   TYR N  95 
 ARG   0.007   0.000   ARG A 317 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A  268 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7138 (tt0)
REVERT: A  314 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7943 (mm-30)
REVERT: N   43 LYS cc_start: 0.7570 (mtpp) cc_final: 0.6799 (mmtp)
REVERT: R  735 THR cc_start: 0.8030 (m) cc_final: 0.7690 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 114
  average time/residue: 1.1672
  time to fit residues: 141.8525
Evaluate side-chains
  116 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain R residue  566 LEU
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  757 LEU
Chi-restraints excluded: chain R residue  777 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 66 optimal weight:    0.8980
   chunk 32 optimal weight:    0.2980
   chunk 23 optimal weight:   10.0000
   chunk 40 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0070
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R 562 HIS
R 672 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.167960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.128865 restraints weight = 8089.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.92
r_work: 0.3329 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7992  Z= 0.156
  Angle     :  0.499   7.404  10845  Z= 0.265
  Chirality :  0.041   0.162   1236
  Planarity :  0.003   0.038   1385
  Dihedral  :  4.157  34.703   1095
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 22.79 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    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:  0.89 (0.27), residues: 998
  helix:  2.06 (0.28), residues: 362
  sheet:  0.27 (0.33), residues: 209
  loop : -0.50 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.009   0.001   TYR R 602 
 ARG   0.007   0.000   ARG A 317 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6565.65 seconds
wall clock time: 115 minutes 25.03 seconds (6925.03 seconds total)