Starting phenix.real_space_refine
on Tue Mar 11 23:23:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ikl_35516/03_2025/8ikl_35516.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ikl_35516/03_2025/8ikl_35516.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ikl_35516/03_2025/8ikl_35516.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ikl_35516/03_2025/8ikl_35516.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ikl_35516/03_2025/8ikl_35516.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ikl_35516/03_2025/8ikl_35516.cif"
  }
  resolution = 2.33
  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=   0.026
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      48      5.16       5
     C    4434      2.51       5
     N    1197      2.21       5
     O    1263      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6942
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "R"
      Number of atoms: 2173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2173
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 5, 'TRANS': 265}
    Chain: "A"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1761
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 209}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "Y"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
  Time building chain proxies: 4.51, per 1000 atoms: 0.65
  Number of scatterers: 6942
  At special positions: 0
  Unit cell: (124.62, 93.93, 93, 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      48     16.00
     O    1263      8.00
     N    1197      7.00
     C    4434      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 612 " - pdb=" SG  CYS R 684 " 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: 1.73
  Conformation dependent library (CDL) restraints added in 952.5 milliseconds
  

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1642

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      47.8% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'R' and resid 532 through 537
    Processing helix  chain 'R' and resid 544 through 572
    Processing helix  chain 'R' and resid 573 through 576
    Processing helix  chain 'R' and resid 577 through 601
    Processing helix  chain 'R' and resid 609 through 642
    Processing helix  chain 'R' and resid 651 through 674
      Proline residue:  R 663  - end of helix
    Processing helix  chain 'R' and resid 675 through 678
    Processing helix  chain 'R' and resid 693 through 726
      Proline residue:  R 699  - end of helix
      removed outlier: 4.851A  pdb=" N   SER R 723 " --> pdb=" O   THR R 719 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   GLU R 724 " --> pdb=" O   GLN R 720 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 731 through 750
    Processing helix  chain 'R' and resid 751 through 759
      removed outlier: 4.051A  pdb=" N   PHE R 755 " --> pdb=" O   THR R 752 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   PHE R 758 " --> pdb=" O   PHE R 755 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE R 759 " --> pdb=" O   GLY R 756 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 761 through 763
      No H-bonds generated for 'chain 'R' and resid 761 through 763'
    Processing helix  chain 'R' and resid 764 through 777
      removed outlier: 3.561A  pdb=" N   LEU R 777 " --> pdb=" O   ILE R 773 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 777 through 788
    Processing helix  chain 'R' and resid 790 through 801
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.873A  pdb=" N   THR A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   TYR A  29 " --> pdb=" O   ARG A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 93 through 99
    Processing helix  chain 'A' and resid 117 through 130
      removed outlier: 3.569A  pdb=" N   ASN A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 153
      removed outlier: 3.501A  pdb=" N   GLU A 150 " --> pdb=" O   THR A 146 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLU A 151 " --> pdb=" O   ASP A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 161
    Processing helix  chain 'A' and resid 171 through 186
      removed outlier: 3.587A  pdb=" N   LYS A 186 " --> pdb=" O   CYS A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 228
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.568A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'Y' and resid 10 through 24
    Processing helix  chain 'Y' and resid 29 through 44
    Processing helix  chain 'Y' and resid 45 through 48
    Processing helix  chain 'Y' and resid 55 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76
      removed outlier: 6.560A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A  82 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   VAL A  84 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ILE A  36 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   VAL A  86 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU A  38 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LYS A  35 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   LEU A 107 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   LEU A  37 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   LEU A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.110A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.593A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.944A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.446A  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: 6.549A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.145A  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: 6.668A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.437A  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: 6.639A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.550A  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: 3.658A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1047 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: 2.11

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2259
        1.34 -     1.46: 1405
        1.46 -     1.58: 3351
        1.58 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 7079
  Sorted by residual:
  bond pdb=" CG  PRO R 663 "
       pdb=" CD  PRO R 663 "
    ideal  model  delta    sigma   weight residual
    1.503  1.472  0.031 3.40e-02 8.65e+02 8.36e-01
  bond pdb=" CB  ASP B 163 "
       pdb=" CG  ASP B 163 "
    ideal  model  delta    sigma   weight residual
    1.516  1.493  0.023 2.50e-02 1.60e+03 8.30e-01
  bond pdb=" CB  CYS R 565 "
       pdb=" SG  CYS R 565 "
    ideal  model  delta    sigma   weight residual
    1.808  1.778  0.030 3.30e-02 9.18e+02 8.13e-01
  bond pdb=" CG  ARG R 613 "
       pdb=" CD  ARG R 613 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 3.00e-02 1.11e+03 7.65e-01
  bond pdb=" CG1 ILE B  43 "
       pdb=" CD1 ILE B  43 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.89e-01
  ... (remaining 7074 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 9219
        1.23 -     2.46: 293
        2.46 -     3.69: 48
        3.69 -     4.92: 10
        4.92 -     6.14: 5
  Bond angle restraints: 9575
  Sorted by residual:
  angle pdb=" CA  ARG A  32 "
        pdb=" CB  ARG A  32 "
        pdb=" CG  ARG A  32 "
      ideal   model   delta    sigma   weight residual
     114.10  120.24   -6.14 2.00e+00 2.50e-01 9.44e+00
  angle pdb=" C   SER A  91 "
        pdb=" N   GLU A  92 "
        pdb=" CA  GLU A  92 "
      ideal   model   delta    sigma   weight residual
     122.08  126.38   -4.30 1.47e+00 4.63e-01 8.55e+00
  angle pdb=" C   VAL A  13 "
        pdb=" CA  VAL A  13 "
        pdb=" CB  VAL A  13 "
      ideal   model   delta    sigma   weight residual
     112.14  108.91    3.23 1.35e+00 5.49e-01 5.74e+00
  angle pdb=" N   GLY R 600 "
        pdb=" CA  GLY R 600 "
        pdb=" C   GLY R 600 "
      ideal   model   delta    sigma   weight residual
     113.18  118.33   -5.15 2.37e+00 1.78e-01 4.72e+00
  angle pdb=" N   ARG A  32 "
        pdb=" CA  ARG A  32 "
        pdb=" CB  ARG A  32 "
      ideal   model   delta    sigma   weight residual
     110.98  107.65    3.33 1.65e+00 3.67e-01 4.06e+00
  ... (remaining 9570 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3883
       17.91 -    35.82: 277
       35.82 -    53.72: 32
       53.72 -    71.63: 7
       71.63 -    89.54: 5
  Dihedral angle restraints: 4204
    sinusoidal: 1669
      harmonic: 2535
  Sorted by residual:
  dihedral pdb=" CB  CYS R 612 "
           pdb=" SG  CYS R 612 "
           pdb=" SG  CYS R 684 "
           pdb=" CB  CYS R 684 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.47   35.47     1      1.00e+01 1.00e-02 1.78e+01
  dihedral pdb=" CA  ARG R 643 "
           pdb=" C   ARG R 643 "
           pdb=" N   VAL R 644 "
           pdb=" CA  VAL R 644 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.22  -18.78     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  PHE A 134 "
           pdb=" C   PHE A 134 "
           pdb=" N   SER A 135 "
           pdb=" CA  SER A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.39   17.61     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 4201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 598
       0.028 -    0.055: 312
       0.055 -    0.083: 111
       0.083 -    0.110: 54
       0.110 -    0.138: 19
  Chirality restraints: 1094
  Sorted by residual:
  chirality pdb=" CA  ILE A  36 "
            pdb=" N   ILE A  36 "
            pdb=" C   ILE A  36 "
            pdb=" CB  ILE A  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CB  VAL A 137 "
            pdb=" CA  VAL A 137 "
            pdb=" CG1 VAL A 137 "
            pdb=" CG2 VAL A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 1091 not shown)

  Planarity restraints: 1208
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.035 5.00e-02 4.00e+02   5.31e-02 4.52e+00
        pdb=" N   PRO B 236 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL Y  54 "   -0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO Y  55 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO Y  55 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO Y  55 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN R 745 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.84e+00
        pdb=" CD  GLN R 745 "    0.023 2.00e-02 2.50e+03
        pdb=" OE1 GLN R 745 "   -0.009 2.00e-02 2.50e+03
        pdb=" NE2 GLN R 745 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1205 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 371
        2.73 -     3.27: 6774
        3.27 -     3.82: 11586
        3.82 -     4.36: 14280
        4.36 -     4.90: 24581
  Nonbonded interactions: 57592
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   ILE R 575 "
            pdb=" OG1 THR R 580 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ALA R 671 "
            pdb=" OG  SER R 675 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.260 3.040
  ... (remaining 57587 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:             0.470
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.230
  Find NCS groups from input model:        0.070
  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:14.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
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   0.039   7079  Z= 0.233
  Angle     :  0.532   6.144   9575  Z= 0.295
  Chirality :  0.042   0.138   1094
  Planarity :  0.004   0.053   1208
  Dihedral  : 12.536  89.540   2559
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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:  1.25 (0.29), residues: 865
  helix:  2.32 (0.27), residues: 361
  sheet:  0.48 (0.40), residues: 165
  loop : -0.64 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 221 
 PHE   0.021   0.002   PHE R 722 
 TYR   0.011   0.002   TYR B  59 
 ARG   0.008   0.000   ARG A  32 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.812 
Fit side-chains
REVERT: R  558 SER cc_start: 0.8105 (m) cc_final: 0.7871 (m)
REVERT: B  258 ASP cc_start: 0.7418 (t0) cc_final: 0.6802 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 1.3216
  time to fit residues: 211.8621
Evaluate side-chains
  145 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0270
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0970
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
R 576 GLN
R 745 GLN
A 144 ASN
B 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.132476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.115642 restraints weight = 8461.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.45
r_work: 0.3473 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7079  Z= 0.172
  Angle     :  0.478   6.212   9575  Z= 0.262
  Chirality :  0.040   0.137   1094
  Planarity :  0.003   0.050   1208
  Dihedral  :  4.277  32.463    946
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  7.12 %
    Favored  : 91.95 %
  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:  1.66 (0.30), residues: 865
  helix:  2.69 (0.27), residues: 366
  sheet:  0.44 (0.39), residues: 177
  loop : -0.36 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.012   0.001   PHE R 623 
 TYR   0.010   0.001   TYR R 683 
 ARG   0.003   0.000   ARG A 184 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 154
  time to evaluate  : 0.743 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8038 (t0) cc_final: 0.7435 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 156
  average time/residue: 1.2622
  time to fit residues: 207.0254
Evaluate side-chains
  151 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 147
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue  135 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0870
   chunk 46 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN
A 144 ASN
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.132104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.114959 restraints weight = 8570.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.47
r_work: 0.3457 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7079  Z= 0.207
  Angle     :  0.481   6.024   9575  Z= 0.263
  Chirality :  0.040   0.133   1094
  Planarity :  0.004   0.049   1208
  Dihedral  :  4.267  30.648    946
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  9.50 %
    Favored  : 88.92 %
  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:  1.65 (0.29), residues: 865
  helix:  2.78 (0.27), residues: 366
  sheet:  0.39 (0.40), residues: 172
  loop : -0.47 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 221 
 PHE   0.016   0.002   PHE A  49 
 TYR   0.012   0.001   TYR R 621 
 ARG   0.008   0.000   ARG B 219 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 0.854 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8072 (t0) cc_final: 0.7416 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 157
  average time/residue: 1.2016
  time to fit residues: 198.6189
Evaluate side-chains
  157 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 152
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  156 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.131882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.114710 restraints weight = 8579.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.47
r_work: 0.3450 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7079  Z= 0.219
  Angle     :  0.485   6.155   9575  Z= 0.263
  Chirality :  0.041   0.132   1094
  Planarity :  0.004   0.050   1208
  Dihedral  :  4.265  27.746    946
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.55 %
    Favored  : 87.60 %
  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:  1.69 (0.29), residues: 865
  helix:  2.87 (0.27), residues: 366
  sheet:  0.36 (0.40), residues: 172
  loop : -0.50 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 221 
 PHE   0.015   0.002   PHE R 623 
 TYR   0.012   0.001   TYR R 621 
 ARG   0.005   0.000   ARG B 219 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 0.863 
Fit side-chains
REVERT: R  624 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8589 (mp)
REVERT: B  258 ASP cc_start: 0.8068 (t0) cc_final: 0.7402 (t0)
  outliers start: 14
  outliers final: 8
  residues processed: 160
  average time/residue: 1.2384
  time to fit residues: 208.3336
Evaluate side-chains
  160 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  615 VAL
Chi-restraints excluded: chain R residue  624 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  156 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0170
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.1022

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN
R 775 ASN
R 778 GLN
A 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.130262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.113108 restraints weight = 8412.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.45
r_work: 0.3427 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7079  Z= 0.310
  Angle     :  0.534   7.016   9575  Z= 0.287
  Chirality :  0.043   0.135   1094
  Planarity :  0.004   0.051   1208
  Dihedral  :  4.454  25.163    946
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.08 %
    Favored  : 86.81 %
  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:  1.54 (0.29), residues: 865
  helix:  2.70 (0.27), residues: 366
  sheet:  0.27 (0.40), residues: 173
  loop : -0.52 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 221 
 PHE   0.018   0.002   PHE R 623 
 TYR   0.018   0.002   TYR B 145 
 ARG   0.004   0.000   ARG B 219 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.723 
Fit side-chains
REVERT: R  624 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8579 (mp)
REVERT: B  258 ASP cc_start: 0.8073 (t0) cc_final: 0.7447 (t70)
  outliers start: 16
  outliers final: 7
  residues processed: 151
  average time/residue: 1.3063
  time to fit residues: 206.8023
Evaluate side-chains
  154 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  610 LEU
Chi-restraints excluded: chain R residue  615 VAL
Chi-restraints excluded: chain R residue  624 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  156 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0670
   chunk 10 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.131543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.114302 restraints weight = 8523.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.47
r_work: 0.3455 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7079  Z= 0.187
  Angle     :  0.468   6.321   9575  Z= 0.256
  Chirality :  0.040   0.139   1094
  Planarity :  0.004   0.047   1208
  Dihedral  :  4.202  23.412    946
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.80 %
    Favored  : 85.75 %
  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:  1.63 (0.30), residues: 865
  helix:  2.90 (0.27), residues: 366
  sheet:  0.19 (0.40), residues: 172
  loop : -0.55 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.015   0.001   PHE A  74 
 TYR   0.011   0.001   TYR B 145 
 ARG   0.006   0.000   ARG B 219 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.797 
Fit side-chains
REVERT: R  624 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8586 (mp)
REVERT: A   71 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7182 (mt-10)
REVERT: B  258 ASP cc_start: 0.8053 (t0) cc_final: 0.7494 (t70)
  outliers start: 11
  outliers final: 4
  residues processed: 155
  average time/residue: 1.2089
  time to fit residues: 197.2333
Evaluate side-chains
  159 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 154
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  624 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue   42 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 72 optimal weight:    0.0040
   chunk 9 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0030
   overall best weight:    0.4602

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.132460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.115398 restraints weight = 8431.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.45
r_work: 0.3464 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7079  Z= 0.170
  Angle     :  0.458   6.250   9575  Z= 0.249
  Chirality :  0.040   0.146   1094
  Planarity :  0.003   0.046   1208
  Dihedral  :  4.096  21.809    946
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 13.72 %
    Favored  : 85.22 %
  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:  1.70 (0.30), residues: 865
  helix:  2.98 (0.27), residues: 366
  sheet:  0.10 (0.39), residues: 177
  loop : -0.47 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.018   0.001   PHE A  49 
 TYR   0.010   0.001   TYR B 145 
 ARG   0.006   0.000   ARG B 219 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 0.736 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8033 (t0) cc_final: 0.7386 (t70)
  outliers start: 8
  outliers final: 2
  residues processed: 152
  average time/residue: 1.2333
  time to fit residues: 197.0469
Evaluate side-chains
  151 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue   42 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R 576 GLN
R 745 GLN
A 144 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.131858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.114705 restraints weight = 8462.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.46
r_work: 0.3451 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7079  Z= 0.207
  Angle     :  0.486   6.052   9575  Z= 0.261
  Chirality :  0.041   0.143   1094
  Planarity :  0.003   0.047   1208
  Dihedral  :  4.160  21.884    946
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 13.46 %
    Favored  : 85.49 %
  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:  1.65 (0.30), residues: 865
  helix:  2.95 (0.27), residues: 366
  sheet:  0.06 (0.39), residues: 172
  loop : -0.50 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 221 
 PHE   0.019   0.002   PHE A  74 
 TYR   0.014   0.001   TYR B 145 
 ARG   0.005   0.000   ARG B 219 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.801 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8046 (t0) cc_final: 0.7437 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 156
  average time/residue: 1.2797
  time to fit residues: 209.8352
Evaluate side-chains
  157 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  765 LEU
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 37 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0050
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.132469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.115248 restraints weight = 8502.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.46
r_work: 0.3462 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7079  Z= 0.172
  Angle     :  0.466   6.181   9575  Z= 0.253
  Chirality :  0.040   0.152   1094
  Planarity :  0.003   0.046   1208
  Dihedral  :  4.220  36.227    946
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.51 %
    Favored  : 84.56 %
  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:  1.69 (0.30), residues: 865
  helix:  3.01 (0.27), residues: 366
  sheet: -0.03 (0.39), residues: 177
  loop : -0.43 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.020   0.001   PHE A  74 
 TYR   0.012   0.001   TYR B 145 
 ARG   0.005   0.000   ARG B 219 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 0.764 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8042 (t0) cc_final: 0.7436 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 153
  average time/residue: 1.2706
  time to fit residues: 204.1073
Evaluate side-chains
  154 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 149
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN
R 775 ASN
A 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.131034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.113678 restraints weight = 8552.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.47
r_work: 0.3437 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7079  Z= 0.271
  Angle     :  0.528   6.188   9575  Z= 0.280
  Chirality :  0.043   0.183   1094
  Planarity :  0.004   0.046   1208
  Dihedral  :  4.490  45.508    946
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 14.64 %
    Favored  : 84.70 %
  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:  1.57 (0.30), residues: 865
  helix:  2.85 (0.26), residues: 366
  sheet: -0.11 (0.39), residues: 180
  loop : -0.42 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  99 
 HIS   0.005   0.001   HIS A 221 
 PHE   0.020   0.002   PHE A  74 
 TYR   0.017   0.001   TYR B 145 
 ARG   0.005   0.000   ARG B 219 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 152
  time to evaluate  : 0.835 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8044 (t0) cc_final: 0.7411 (t70)
  outliers start: 5
  outliers final: 4
  residues processed: 152
  average time/residue: 1.3194
  time to fit residues: 210.1395
Evaluate side-chains
  155 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  163 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
R 775 ASN
A 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.130438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.113192 restraints weight = 8490.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.45
r_work: 0.3430 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7079  Z= 0.298
  Angle     :  0.542   6.604   9575  Z= 0.288
  Chirality :  0.044   0.192   1094
  Planarity :  0.004   0.047   1208
  Dihedral  :  4.485  34.563    946
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.54 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 14.78 %
    Favored  : 84.70 %
  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:  1.44 (0.29), residues: 865
  helix:  2.76 (0.26), residues: 365
  sheet: -0.14 (0.39), residues: 180
  loop : -0.51 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 221 
 PHE   0.019   0.002   PHE A  74 
 TYR   0.019   0.002   TYR B 145 
 ARG   0.007   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7010.11 seconds
wall clock time: 119 minutes 45.18 seconds (7185.18 seconds total)