Starting phenix.real_space_refine
on Thu Feb  5 05:38:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9my4_48726/02_2026/9my4_48726.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9my4_48726/02_2026/9my4_48726.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9my4_48726/02_2026/9my4_48726.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9my4_48726/02_2026/9my4_48726.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9my4_48726/02_2026/9my4_48726.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9my4_48726/02_2026/9my4_48726.cif"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.017
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      72      5.16       5
     C    9724      2.51       5
     N    2536      2.21       5
     O    2660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14992
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2718
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 331}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 33
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "B"
      Number of atoms: 1030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1030
          Classifications: {'peptide': 137}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 2, 'TRANS': 134}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 41
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 30
  Restraints were copied for chains:
    C, E, G, D, F, H
  Time building chain proxies: 2.30, per 1000 atoms: 0.15
  Number of scatterers: 14992
  At special positions: 0
  Unit cell: (114.24, 114.24, 126.72, 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      72     16.00
     O    2660      8.00
     N    2536      7.00
     C    9724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 581.6 milliseconds
  

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3544

  Finding SS restraints...
    Secondary structure from input PDB file:
      100 helices and 4 sheets defined
      78.6% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 105
    Processing helix  chain 'A' and resid 109 through 135
      removed outlier: 4.207A  pdb=" N   TYR A 115 " --> pdb=" O   LYS A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 168
      removed outlier: 4.222A  pdb=" N   LEU A 146 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 171
      No H-bonds generated for 'chain 'A' and resid 169 through 171'
    Processing helix  chain 'A' and resid 176 through 185
      removed outlier: 3.880A  pdb=" N   LEU A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ARG A 182 " --> pdb=" O   TRP A 178 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 205
      removed outlier: 3.974A  pdb=" N   ILE A 191 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASP A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 224
      removed outlier: 4.196A  pdb=" N   PHE A 222 " --> pdb=" O   ARG A 218 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 235 through 248
      removed outlier: 3.621A  pdb=" N   SER A 243 " --> pdb=" O   ARG A 239 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   HIS A 248 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 274
      removed outlier: 3.681A  pdb=" N   PHE A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 300
    Processing helix  chain 'A' and resid 312 through 348
      removed outlier: 3.953A  pdb=" N   VAL A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   PHE A 325 " --> pdb=" O   CYS A 321 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   SER A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   PHE A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 353 through 356
    Processing helix  chain 'A' and resid 357 through 374
    Processing helix  chain 'A' and resid 379 through 384
    Processing helix  chain 'A' and resid 498 through 521
      removed outlier: 3.539A  pdb=" N   ALA A 502 " --> pdb=" O   HIS A 498 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LYS A 504 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 553
      removed outlier: 3.897A  pdb=" N   VAL A 530 " --> pdb=" O   ASP A 526 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER A 535 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG A 544 " --> pdb=" O   ASN A 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 21
      removed outlier: 4.194A  pdb=" N   ALA B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU B  19 " --> pdb=" O   GLU B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 3.957A  pdb=" N   SER B  39 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 55
      removed outlier: 3.742A  pdb=" N   GLU B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 74
    Processing helix  chain 'B' and resid 79 through 93
      removed outlier: 3.762A  pdb=" N   GLU B  85 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 113
    Processing helix  chain 'B' and resid 118 through 128
    Processing helix  chain 'B' and resid 138 through 146
      removed outlier: 4.380A  pdb=" N   GLN B 144 " --> pdb=" O   GLU B 140 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET B 145 " --> pdb=" O   GLU B 141 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 105
    Processing helix  chain 'C' and resid 109 through 135
      removed outlier: 4.207A  pdb=" N   TYR C 115 " --> pdb=" O   LYS C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 168
      removed outlier: 4.222A  pdb=" N   LEU C 146 " --> pdb=" O   ALA C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 171
      No H-bonds generated for 'chain 'C' and resid 169 through 171'
    Processing helix  chain 'C' and resid 176 through 185
      removed outlier: 3.880A  pdb=" N   LEU C 181 " --> pdb=" O   VAL C 177 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ARG C 182 " --> pdb=" O   TRP C 178 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE C 183 " --> pdb=" O   GLY C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 205
      removed outlier: 3.974A  pdb=" N   ILE C 191 " --> pdb=" O   PRO C 187 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASP C 192 " --> pdb=" O   ILE C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 224
      removed outlier: 4.196A  pdb=" N   PHE C 222 " --> pdb=" O   ARG C 218 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN C 224 " --> pdb=" O   ILE C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 230
    Processing helix  chain 'C' and resid 235 through 248
      removed outlier: 3.621A  pdb=" N   SER C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL C 244 " --> pdb=" O   LEU C 240 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   HIS C 248 " --> pdb=" O   VAL C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 274
      removed outlier: 3.681A  pdb=" N   PHE C 269 " --> pdb=" O   PHE C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 300
    Processing helix  chain 'C' and resid 312 through 348
      removed outlier: 3.953A  pdb=" N   VAL C 324 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   PHE C 325 " --> pdb=" O   CYS C 321 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   SER C 328 " --> pdb=" O   VAL C 324 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   PHE C 329 " --> pdb=" O   PHE C 325 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE C 330 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
      Proline residue:  C 333  - end of helix
    Processing helix  chain 'C' and resid 353 through 356
    Processing helix  chain 'C' and resid 357 through 374
    Processing helix  chain 'C' and resid 379 through 384
    Processing helix  chain 'C' and resid 498 through 521
      removed outlier: 3.539A  pdb=" N   ALA C 502 " --> pdb=" O   HIS C 498 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LYS C 504 " --> pdb=" O   ARG C 500 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 526 through 553
      removed outlier: 3.897A  pdb=" N   VAL C 530 " --> pdb=" O   ASP C 526 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER C 535 " --> pdb=" O   ILE C 531 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG C 544 " --> pdb=" O   ASN C 540 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 21
      removed outlier: 4.194A  pdb=" N   ALA D  16 " --> pdb=" O   GLU D  12 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU D  19 " --> pdb=" O   GLU D  15 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 39
      removed outlier: 3.957A  pdb=" N   SER D  39 " --> pdb=" O   THR D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 55
      removed outlier: 3.742A  pdb=" N   GLU D  55 " --> pdb=" O   ASP D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 74
    Processing helix  chain 'D' and resid 79 through 93
      removed outlier: 3.762A  pdb=" N   GLU D  85 " --> pdb=" O   ASP D  81 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE D  93 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 113
    Processing helix  chain 'D' and resid 118 through 128
    Processing helix  chain 'D' and resid 138 through 146
      removed outlier: 4.380A  pdb=" N   GLN D 144 " --> pdb=" O   GLU D 140 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET D 145 " --> pdb=" O   GLU D 141 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET D 146 " --> pdb=" O   PHE D 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 105
    Processing helix  chain 'E' and resid 109 through 135
      removed outlier: 4.207A  pdb=" N   TYR E 115 " --> pdb=" O   LYS E 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 138 through 168
      removed outlier: 4.222A  pdb=" N   LEU E 146 " --> pdb=" O   ALA E 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 169 through 171
      No H-bonds generated for 'chain 'E' and resid 169 through 171'
    Processing helix  chain 'E' and resid 176 through 185
      removed outlier: 3.880A  pdb=" N   LEU E 181 " --> pdb=" O   VAL E 177 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ARG E 182 " --> pdb=" O   TRP E 178 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE E 183 " --> pdb=" O   GLY E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 186 through 205
      removed outlier: 3.974A  pdb=" N   ILE E 191 " --> pdb=" O   PRO E 187 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASP E 192 " --> pdb=" O   ILE E 188 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 217 through 224
      removed outlier: 4.196A  pdb=" N   PHE E 222 " --> pdb=" O   ARG E 218 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN E 224 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 225 through 230
    Processing helix  chain 'E' and resid 235 through 248
      removed outlier: 3.621A  pdb=" N   SER E 243 " --> pdb=" O   ARG E 239 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL E 244 " --> pdb=" O   LEU E 240 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   HIS E 248 " --> pdb=" O   VAL E 244 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 274
      removed outlier: 3.681A  pdb=" N   PHE E 269 " --> pdb=" O   PHE E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 288 through 300
    Processing helix  chain 'E' and resid 312 through 348
      removed outlier: 3.953A  pdb=" N   VAL E 324 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   PHE E 325 " --> pdb=" O   CYS E 321 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   SER E 328 " --> pdb=" O   VAL E 324 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   PHE E 329 " --> pdb=" O   PHE E 325 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE E 330 " --> pdb=" O   ALA E 326 " (cutoff:3.500A)
      Proline residue:  E 333  - end of helix
    Processing helix  chain 'E' and resid 353 through 356
    Processing helix  chain 'E' and resid 357 through 374
    Processing helix  chain 'E' and resid 379 through 384
    Processing helix  chain 'E' and resid 498 through 521
      removed outlier: 3.539A  pdb=" N   ALA E 502 " --> pdb=" O   HIS E 498 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LYS E 504 " --> pdb=" O   ARG E 500 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 526 through 553
      removed outlier: 3.897A  pdb=" N   VAL E 530 " --> pdb=" O   ASP E 526 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER E 535 " --> pdb=" O   ILE E 531 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG E 544 " --> pdb=" O   ASN E 540 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 12 through 21
      removed outlier: 4.194A  pdb=" N   ALA F  16 " --> pdb=" O   GLU F  12 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU F  19 " --> pdb=" O   GLU F  15 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 39
      removed outlier: 3.957A  pdb=" N   SER F  39 " --> pdb=" O   THR F  35 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 55
      removed outlier: 3.742A  pdb=" N   GLU F  55 " --> pdb=" O   ASP F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 74
    Processing helix  chain 'F' and resid 79 through 93
      removed outlier: 3.762A  pdb=" N   GLU F  85 " --> pdb=" O   ASP F  81 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 113
    Processing helix  chain 'F' and resid 118 through 128
    Processing helix  chain 'F' and resid 138 through 146
      removed outlier: 4.380A  pdb=" N   GLN F 144 " --> pdb=" O   GLU F 140 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET F 145 " --> pdb=" O   GLU F 141 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET F 146 " --> pdb=" O   PHE F 142 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 96 through 105
    Processing helix  chain 'G' and resid 109 through 135
      removed outlier: 4.207A  pdb=" N   TYR G 115 " --> pdb=" O   LYS G 111 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 138 through 168
      removed outlier: 4.222A  pdb=" N   LEU G 146 " --> pdb=" O   ALA G 142 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 169 through 171
      No H-bonds generated for 'chain 'G' and resid 169 through 171'
    Processing helix  chain 'G' and resid 176 through 185
      removed outlier: 3.880A  pdb=" N   LEU G 181 " --> pdb=" O   VAL G 177 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ARG G 182 " --> pdb=" O   TRP G 178 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE G 183 " --> pdb=" O   GLY G 179 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 186 through 205
      removed outlier: 3.974A  pdb=" N   ILE G 191 " --> pdb=" O   PRO G 187 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASP G 192 " --> pdb=" O   ILE G 188 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 217 through 224
      removed outlier: 4.196A  pdb=" N   PHE G 222 " --> pdb=" O   ARG G 218 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN G 224 " --> pdb=" O   ILE G 220 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 225 through 230
    Processing helix  chain 'G' and resid 235 through 248
      removed outlier: 3.621A  pdb=" N   SER G 243 " --> pdb=" O   ARG G 239 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL G 244 " --> pdb=" O   LEU G 240 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   HIS G 248 " --> pdb=" O   VAL G 244 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 248 through 274
      removed outlier: 3.681A  pdb=" N   PHE G 269 " --> pdb=" O   PHE G 265 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 288 through 300
    Processing helix  chain 'G' and resid 312 through 348
      removed outlier: 3.953A  pdb=" N   VAL G 324 " --> pdb=" O   SER G 320 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   PHE G 325 " --> pdb=" O   CYS G 321 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   SER G 328 " --> pdb=" O   VAL G 324 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   PHE G 329 " --> pdb=" O   PHE G 325 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE G 330 " --> pdb=" O   ALA G 326 " (cutoff:3.500A)
      Proline residue:  G 333  - end of helix
    Processing helix  chain 'G' and resid 353 through 356
    Processing helix  chain 'G' and resid 357 through 374
    Processing helix  chain 'G' and resid 379 through 384
    Processing helix  chain 'G' and resid 498 through 521
      removed outlier: 3.539A  pdb=" N   ALA G 502 " --> pdb=" O   HIS G 498 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LYS G 504 " --> pdb=" O   ARG G 500 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 526 through 553
      removed outlier: 3.897A  pdb=" N   VAL G 530 " --> pdb=" O   ASP G 526 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER G 535 " --> pdb=" O   ILE G 531 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG G 544 " --> pdb=" O   ASN G 540 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 12 through 21
      removed outlier: 4.194A  pdb=" N   ALA H  16 " --> pdb=" O   GLU H  12 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU H  19 " --> pdb=" O   GLU H  15 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 39
      removed outlier: 3.957A  pdb=" N   SER H  39 " --> pdb=" O   THR H  35 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 45 through 55
      removed outlier: 3.742A  pdb=" N   GLU H  55 " --> pdb=" O   ASP H  51 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 66 through 74
    Processing helix  chain 'H' and resid 79 through 93
      removed outlier: 3.762A  pdb=" N   GLU H  85 " --> pdb=" O   ASP H  81 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE H  93 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 102 through 113
    Processing helix  chain 'H' and resid 118 through 128
    Processing helix  chain 'H' and resid 138 through 146
      removed outlier: 4.380A  pdb=" N   GLN H 144 " --> pdb=" O   GLU H 140 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET H 145 " --> pdb=" O   GLU H 141 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET H 146 " --> pdb=" O   PHE H 142 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28
    Processing sheet with id=AA2, first strand: chain 'D' and resid 27 through 28
    Processing sheet with id=AA3, first strand: chain 'F' and resid 27 through 28
    Processing sheet with id=AA4, first strand: chain 'H' and resid 27 through 28

    977 hydrogen bonds defined for protein.
    2871 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: 2.20

  Time building geometry restraints manager: 1.51 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: 4804
        1.34 -     1.46: 3560
        1.46 -     1.58: 6828
        1.58 -     1.69: 0
        1.69 -     1.81: 124
  Bond restraints: 15316
  Sorted by residual:
  bond pdb=" CG  LEU H  70 "
       pdb=" CD1 LEU H  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.31e+00
  bond pdb=" CG  LEU B  70 "
       pdb=" CD1 LEU B  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.31e+00
  bond pdb=" CG  LEU D  70 "
       pdb=" CD1 LEU D  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.31e+00
  bond pdb=" CG  LEU F  70 "
       pdb=" CD1 LEU F  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.31e+00
  bond pdb=" CG  ARG H 127 "
       pdb=" CD  ARG H 127 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.86e-01
  ... (remaining 15311 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 20456
        2.26 -     4.53: 256
        4.53 -     6.79: 16
        6.79 -     9.05: 4
        9.05 -    11.31: 8
  Bond angle restraints: 20740
  Sorted by residual:
  angle pdb=" CA  LEU H  70 "
        pdb=" CB  LEU H  70 "
        pdb=" CG  LEU H  70 "
      ideal   model   delta    sigma   weight residual
     116.30  127.61  -11.31 3.50e+00 8.16e-02 1.05e+01
  angle pdb=" CA  LEU B  70 "
        pdb=" CB  LEU B  70 "
        pdb=" CG  LEU B  70 "
      ideal   model   delta    sigma   weight residual
     116.30  127.61  -11.31 3.50e+00 8.16e-02 1.05e+01
  angle pdb=" CA  LEU D  70 "
        pdb=" CB  LEU D  70 "
        pdb=" CG  LEU D  70 "
      ideal   model   delta    sigma   weight residual
     116.30  127.61  -11.31 3.50e+00 8.16e-02 1.05e+01
  angle pdb=" CA  LEU F  70 "
        pdb=" CB  LEU F  70 "
        pdb=" CG  LEU F  70 "
      ideal   model   delta    sigma   weight residual
     116.30  127.61  -11.31 3.50e+00 8.16e-02 1.05e+01
  angle pdb=" C   GLN E 357 "
        pdb=" N   ILE E 358 "
        pdb=" CA  ILE E 358 "
      ideal   model   delta    sigma   weight residual
     120.33  122.57   -2.24 8.00e-01 1.56e+00 7.87e+00
  ... (remaining 20735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 7832
       17.39 -    34.78: 844
       34.78 -    52.17: 208
       52.17 -    69.56: 48
       69.56 -    86.95: 4
  Dihedral angle restraints: 8936
    sinusoidal: 3436
      harmonic: 5500
  Sorted by residual:
  dihedral pdb=" CA  TYR C 138 "
           pdb=" C   TYR C 138 "
           pdb=" N   ASN C 139 "
           pdb=" CA  ASN C 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.85  -16.15     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  TYR G 138 "
           pdb=" C   TYR G 138 "
           pdb=" N   ASN G 139 "
           pdb=" CA  ASN G 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.85  -16.15     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  TYR A 138 "
           pdb=" C   TYR A 138 "
           pdb=" N   ASN A 139 "
           pdb=" CA  ASN A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.85  -16.15     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 8933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 1296
       0.024 -    0.047: 532
       0.047 -    0.071: 360
       0.071 -    0.094: 116
       0.094 -    0.118: 40
  Chirality restraints: 2344
  Sorted by residual:
  chirality pdb=" CA  ILE H 101 "
            pdb=" N   ILE H 101 "
            pdb=" C   ILE H 101 "
            pdb=" CB  ILE H 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.48e-01
  chirality pdb=" CA  ILE F 101 "
            pdb=" N   ILE F 101 "
            pdb=" C   ILE F 101 "
            pdb=" CB  ILE F 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.48e-01
  chirality pdb=" CA  ILE B 101 "
            pdb=" N   ILE B 101 "
            pdb=" C   ILE B 101 "
            pdb=" CB  ILE B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 2341 not shown)

  Planarity restraints: 2608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN E 349 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" C   GLN E 349 "    0.020 2.00e-02 2.50e+03
        pdb=" O   GLN E 349 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ARG E 350 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN G 349 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" C   GLN G 349 "    0.020 2.00e-02 2.50e+03
        pdb=" O   GLN G 349 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ARG G 350 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C 349 "    0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" C   GLN C 349 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   GLN C 349 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ARG C 350 "    0.007 2.00e-02 2.50e+03
  ... (remaining 2605 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.01: 8648
        3.01 -     3.48: 16347
        3.48 -     3.95: 22045
        3.95 -     4.43: 25921
        4.43 -     4.90: 39338
  Nonbonded interactions: 112299
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP G 526 "
            pdb=" N   VAL G 527 "
     model   vdw
     2.534 3.120
  nonbonded pdb=" OD1 ASP A 526 "
            pdb=" N   VAL A 527 "
     model   vdw
     2.534 3.120
  nonbonded pdb=" OD1 ASP E 526 "
            pdb=" N   VAL E 527 "
     model   vdw
     2.534 3.120
  nonbonded pdb=" OD1 ASP C 526 "
            pdb=" N   VAL C 527 "
     model   vdw
     2.534 3.120
  nonbonded pdb=" O   GLN A 349 "
            pdb=" OE1 GLN A 349 "
     model   vdw
     2.569 3.040
  ... (remaining 112294 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
}

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 group one per residue
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:             4.200
  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:             0.020
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     12.110
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
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      :  0.003   0.038  15316  Z= 0.141
  Angle     :  0.675  11.314  20740  Z= 0.398
  Chirality :  0.037   0.118   2344
  Planarity :  0.003   0.029   2608
  Dihedral  : 15.425  86.947   5392
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 19.84 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.20), residues: 1872
  helix:  1.58 (0.15), residues: 1328
  sheet:  None (None), residues: 0
  loop : -0.36 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 127 
 TYR   0.012   0.001   TYR G 115 
 PHE   0.015   0.001   PHE E 156 
 TRP   0.012   0.001   TRP G 313 
 HIS   0.002   0.001   HIS G 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (15316)
  covalent geometry    : angle       0.67461 (20740)
  hydrogen bonds       : bond        0.15734 (  977)
  hydrogen bonds       : angle       4.69561 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 278
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.7749 (ppp) cc_final: 0.7504 (ppp)
REVERT: A  349 GLN cc_start: 0.8547 (pp30) cc_final: 0.8327 (pp30)
REVERT: C  149 MET cc_start: 0.7746 (ppp) cc_final: 0.7503 (ppp)
REVERT: C  349 GLN cc_start: 0.8546 (pp30) cc_final: 0.8328 (pp30)
REVERT: E  149 MET cc_start: 0.7750 (ppp) cc_final: 0.7505 (ppp)
REVERT: E  349 GLN cc_start: 0.8554 (pp30) cc_final: 0.8336 (pp30)
REVERT: G  149 MET cc_start: 0.7750 (ppp) cc_final: 0.7505 (ppp)
REVERT: G  349 GLN cc_start: 0.8555 (pp30) cc_final: 0.8338 (pp30)
  outliers start: 20
  outliers final: 8
  residues processed: 290
  average time/residue: 0.1283
  time to fit residues: 53.1860
Evaluate side-chains
  236 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 228
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain E residue  301 THR
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  301 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0870
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.7958

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN
** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  54 ASN
** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.124230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.085665 restraints weight = 36772.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.088308 restraints weight = 19027.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.089217 restraints weight = 12708.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.089593 restraints weight = 11416.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.089687 restraints weight = 11170.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.0999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  15316  Z= 0.123
  Angle     :  0.514   8.105  20740  Z= 0.278
  Chirality :  0.037   0.116   2344
  Planarity :  0.003   0.022   2608
  Dihedral  :  4.176  39.372   2076
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 18.15 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.20), residues: 1872
  helix:  1.81 (0.15), residues: 1372
  sheet:  None (None), residues: 0
  loop : -0.69 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  38 
 TYR   0.013   0.001   TYR E 115 
 PHE   0.014   0.001   PHE E 120 
 TRP   0.009   0.001   TRP A 313 
 HIS   0.003   0.001   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (15316)
  covalent geometry    : angle       0.51368 (20740)
  hydrogen bonds       : bond        0.04984 (  977)
  hydrogen bonds       : angle       3.80445 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 263
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 GLN cc_start: 0.8378 (pp30) cc_final: 0.8090 (pp30)
REVERT: B   42 GLN cc_start: 0.8848 (mm110) cc_final: 0.8435 (mm110)
REVERT: B   71 THR cc_start: 0.9115 (m) cc_final: 0.8885 (p)
REVERT: C  349 GLN cc_start: 0.8386 (pp30) cc_final: 0.8096 (pp30)
REVERT: D   42 GLN cc_start: 0.8847 (mm110) cc_final: 0.8435 (mm110)
REVERT: D   71 THR cc_start: 0.9111 (m) cc_final: 0.8881 (p)
REVERT: E  349 GLN cc_start: 0.8386 (pp30) cc_final: 0.8096 (pp30)
REVERT: F   42 GLN cc_start: 0.8851 (mm110) cc_final: 0.8441 (mm110)
REVERT: F   71 THR cc_start: 0.9113 (m) cc_final: 0.8883 (p)
REVERT: G  349 GLN cc_start: 0.8379 (pp30) cc_final: 0.8090 (pp30)
REVERT: H   42 GLN cc_start: 0.8849 (mm110) cc_final: 0.8439 (mm110)
REVERT: H   71 THR cc_start: 0.9086 (m) cc_final: 0.8864 (p)
  outliers start: 24
  outliers final: 4
  residues processed: 275
  average time/residue: 0.1224
  time to fit residues: 48.5688
Evaluate side-chains
  244 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 240
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain F residue   92 VAL
Chi-restraints excluded: chain H residue   92 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 154 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0980
   chunk 21 optimal weight:    0.9980
   chunk 159 optimal weight:    2.9990
   chunk 178 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 158 optimal weight:    0.9990
   chunk 150 optimal weight:    0.0870
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN
C 224 GLN
E 224 GLN
F  54 ASN
G 224 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.130294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.091164 restraints weight = 36570.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.094267 restraints weight = 18880.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.096194 restraints weight = 13247.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.097348 restraints weight = 10844.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.097900 restraints weight = 9710.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  15316  Z= 0.104
  Angle     :  0.472   7.935  20740  Z= 0.255
  Chirality :  0.037   0.116   2344
  Planarity :  0.003   0.024   2608
  Dihedral  :  3.539  13.411   2064
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 17.43 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.20), residues: 1872
  helix:  1.89 (0.15), residues: 1360
  sheet:  None (None), residues: 0
  loop : -0.52 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 127 
 TYR   0.012   0.001   TYR A 115 
 PHE   0.010   0.001   PHE D  93 
 TRP   0.009   0.001   TRP E 369 
 HIS   0.003   0.001   HIS F 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (15316)
  covalent geometry    : angle       0.47192 (20740)
  hydrogen bonds       : bond        0.04199 (  977)
  hydrogen bonds       : angle       3.55170 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 301
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 TRP cc_start: 0.6655 (m-10) cc_final: 0.6083 (m100)
REVERT: A  349 GLN cc_start: 0.8369 (pp30) cc_final: 0.8114 (pp30)
REVERT: A  526 ASP cc_start: 0.8000 (t0) cc_final: 0.7773 (t70)
REVERT: B   14 LYS cc_start: 0.9150 (tptp) cc_final: 0.8918 (tptp)
REVERT: B   45 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8594 (p)
REVERT: B   71 THR cc_start: 0.9054 (m) cc_final: 0.8822 (p)
REVERT: C  148 TRP cc_start: 0.6655 (m-10) cc_final: 0.6084 (m100)
REVERT: C  349 GLN cc_start: 0.8370 (pp30) cc_final: 0.8116 (pp30)
REVERT: C  526 ASP cc_start: 0.8000 (t0) cc_final: 0.7773 (t70)
REVERT: D   14 LYS cc_start: 0.9154 (tptp) cc_final: 0.8921 (tptp)
REVERT: D   45 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8595 (p)
REVERT: D   71 THR cc_start: 0.9055 (m) cc_final: 0.8822 (p)
REVERT: E  148 TRP cc_start: 0.6655 (m-10) cc_final: 0.6084 (m100)
REVERT: E  349 GLN cc_start: 0.8370 (pp30) cc_final: 0.8115 (pp30)
REVERT: E  526 ASP cc_start: 0.7994 (t0) cc_final: 0.7767 (t70)
REVERT: F   14 LYS cc_start: 0.9154 (tptp) cc_final: 0.8923 (tptp)
REVERT: F   45 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8600 (p)
REVERT: F   71 THR cc_start: 0.9052 (m) cc_final: 0.8819 (p)
REVERT: G  148 TRP cc_start: 0.6657 (m-10) cc_final: 0.6086 (m100)
REVERT: G  349 GLN cc_start: 0.8368 (pp30) cc_final: 0.8113 (pp30)
REVERT: G  526 ASP cc_start: 0.7995 (t0) cc_final: 0.7771 (t70)
REVERT: H   14 LYS cc_start: 0.9150 (tptp) cc_final: 0.8918 (tptp)
REVERT: H   45 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8595 (p)
REVERT: H   71 THR cc_start: 0.9063 (m) cc_final: 0.8833 (p)
  outliers start: 21
  outliers final: 13
  residues processed: 314
  average time/residue: 0.1158
  time to fit residues: 53.1135
Evaluate side-chains
  265 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 248
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain D residue   45 THR
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  113 PHE
Chi-restraints excluded: chain F residue   45 THR
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain G residue  105 GLU
Chi-restraints excluded: chain G residue  113 PHE
Chi-restraints excluded: chain H residue   45 THR
Chi-restraints excluded: chain H residue  131 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 9 optimal weight:    0.3980
   chunk 175 optimal weight:   10.0000
   chunk 146 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 69 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 164 optimal weight:    2.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.129812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.091207 restraints weight = 37995.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.094101 restraints weight = 19732.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.095870 restraints weight = 13946.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.096994 restraints weight = 11543.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.097439 restraints weight = 10364.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15316  Z= 0.138
  Angle     :  0.511   8.513  20740  Z= 0.269
  Chirality :  0.038   0.113   2344
  Planarity :  0.003   0.023   2608
  Dihedral  :  3.519  13.484   2064
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.02 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.20), residues: 1872
  helix:  1.98 (0.15), residues: 1360
  sheet:  None (None), residues: 0
  loop : -0.57 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  38 
 TYR   0.010   0.001   TYR A 115 
 PHE   0.007   0.001   PHE E 518 
 TRP   0.011   0.001   TRP A 369 
 HIS   0.002   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (15316)
  covalent geometry    : angle       0.51112 (20740)
  hydrogen bonds       : bond        0.04659 (  977)
  hydrogen bonds       : angle       3.65640 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 257
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 TRP cc_start: 0.6630 (m-10) cc_final: 0.6114 (m100)
REVERT: A  256 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9222 (mt)
REVERT: A  526 ASP cc_start: 0.8171 (t0) cc_final: 0.7828 (t70)
REVERT: B   14 LYS cc_start: 0.9147 (tptp) cc_final: 0.8911 (tptp)
REVERT: B   71 THR cc_start: 0.9015 (m) cc_final: 0.8794 (p)
REVERT: C  148 TRP cc_start: 0.6630 (m-10) cc_final: 0.6116 (m100)
REVERT: C  256 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9220 (mt)
REVERT: C  526 ASP cc_start: 0.8171 (t0) cc_final: 0.7832 (t70)
REVERT: D   14 LYS cc_start: 0.9153 (tptp) cc_final: 0.8915 (tptp)
REVERT: D   71 THR cc_start: 0.9015 (m) cc_final: 0.8795 (p)
REVERT: E  148 TRP cc_start: 0.6637 (m-10) cc_final: 0.6122 (m100)
REVERT: E  256 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9220 (mt)
REVERT: E  526 ASP cc_start: 0.8170 (t0) cc_final: 0.7828 (t70)
REVERT: F   14 LYS cc_start: 0.9152 (tptp) cc_final: 0.8915 (tptp)
REVERT: F   71 THR cc_start: 0.9017 (m) cc_final: 0.8796 (p)
REVERT: G  148 TRP cc_start: 0.6637 (m-10) cc_final: 0.6122 (m100)
REVERT: G  256 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9220 (mt)
REVERT: G  526 ASP cc_start: 0.8175 (t0) cc_final: 0.7830 (t70)
REVERT: H   14 LYS cc_start: 0.9156 (tptp) cc_final: 0.8917 (tptp)
REVERT: H   45 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8683 (p)
REVERT: H   71 THR cc_start: 0.9020 (m) cc_final: 0.8795 (p)
  outliers start: 36
  outliers final: 20
  residues processed: 277
  average time/residue: 0.1176
  time to fit residues: 47.0550
Evaluate side-chains
  261 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 236
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  540 ASN
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  113 PHE
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  540 ASN
Chi-restraints excluded: chain G residue   96 ILE
Chi-restraints excluded: chain G residue  105 GLU
Chi-restraints excluded: chain G residue  113 PHE
Chi-restraints excluded: chain G residue  256 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  540 ASN
Chi-restraints excluded: chain H residue   45 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 138 optimal weight:   10.0000
   chunk 146 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 130 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 162 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
D 108 HIS
F 108 HIS
H 108 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.125814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.085855 restraints weight = 37438.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.088501 restraints weight = 20180.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.090104 restraints weight = 14469.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.090908 restraints weight = 12138.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.091453 restraints weight = 11060.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059  15316  Z= 0.345
  Angle     :  0.698   8.646  20740  Z= 0.373
  Chirality :  0.044   0.139   2344
  Planarity :  0.004   0.027   2608
  Dihedral  :  3.980  13.235   2064
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 17.10 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.20), residues: 1872
  helix:  1.55 (0.14), residues: 1372
  sheet:  None (None), residues: 0
  loop : -0.67 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.019   0.002   TYR D 139 
 PHE   0.017   0.002   PHE H  69 
 TRP   0.012   0.002   TRP E 313 
 HIS   0.004   0.001   HIS C 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00824 (15316)
  covalent geometry    : angle       0.69757 (20740)
  hydrogen bonds       : bond        0.06685 (  977)
  hydrogen bonds       : angle       4.28300 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 225
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 TRP cc_start: 0.6692 (OUTLIER) cc_final: 0.6141 (m100)
REVERT: C  148 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.6141 (m100)
REVERT: E  148 TRP cc_start: 0.6698 (OUTLIER) cc_final: 0.6147 (m100)
REVERT: G  148 TRP cc_start: 0.6695 (OUTLIER) cc_final: 0.6144 (m100)
  outliers start: 66
  outliers final: 54
  residues processed: 273
  average time/residue: 0.1237
  time to fit residues: 48.8601
Evaluate side-chains
  264 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 206
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  148 TRP
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  540 ASN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  148 TRP
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  540 ASN
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  113 PHE
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  148 TRP
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  540 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   59 ASP
Chi-restraints excluded: chain F residue   92 VAL
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain G residue   96 ILE
Chi-restraints excluded: chain G residue  105 GLU
Chi-restraints excluded: chain G residue  113 PHE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain G residue  148 TRP
Chi-restraints excluded: chain G residue  155 VAL
Chi-restraints excluded: chain G residue  163 VAL
Chi-restraints excluded: chain G residue  256 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  540 ASN
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   59 ASP
Chi-restraints excluded: chain H residue   92 VAL
Chi-restraints excluded: chain H residue  131 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 118 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 154 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 135 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 179 optimal weight:    0.9980
   chunk 133 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  50 GLN
** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  50 GLN
** F 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  50 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.129408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.090247 restraints weight = 36641.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.093118 restraints weight = 19070.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.094939 restraints weight = 13503.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.095941 restraints weight = 11137.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.096430 restraints weight = 10001.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15316  Z= 0.128
  Angle     :  0.542   9.144  20740  Z= 0.285
  Chirality :  0.039   0.175   2344
  Planarity :  0.003   0.031   2608
  Dihedral  :  3.705  13.692   2064
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 20.10 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.20), residues: 1872
  helix:  1.94 (0.15), residues: 1372
  sheet:  None (None), residues: 0
  loop : -0.54 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  38 
 TYR   0.015   0.001   TYR A 115 
 PHE   0.007   0.001   PHE H  69 
 TRP   0.013   0.001   TRP E 369 
 HIS   0.002   0.001   HIS E 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (15316)
  covalent geometry    : angle       0.54243 (20740)
  hydrogen bonds       : bond        0.04819 (  977)
  hydrogen bonds       : angle       3.64421 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 237
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 TRP cc_start: 0.6592 (m-10) cc_final: 0.6063 (m100)
REVERT: B   14 LYS cc_start: 0.9110 (tptp) cc_final: 0.8861 (tptp)
REVERT: C  148 TRP cc_start: 0.6591 (m-10) cc_final: 0.6062 (m100)
REVERT: D   14 LYS cc_start: 0.9120 (tptp) cc_final: 0.8868 (tptp)
REVERT: E  148 TRP cc_start: 0.6593 (m-10) cc_final: 0.6063 (m100)
REVERT: F   14 LYS cc_start: 0.9111 (tptp) cc_final: 0.8863 (tptp)
REVERT: G  148 TRP cc_start: 0.6596 (m-10) cc_final: 0.6066 (m100)
REVERT: H   14 LYS cc_start: 0.9110 (tptp) cc_final: 0.8860 (tptp)
  outliers start: 21
  outliers final: 14
  residues processed: 249
  average time/residue: 0.1004
  time to fit residues: 38.4247
Evaluate side-chains
  233 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 219
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  114 VAL
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain G residue   96 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain G residue  300 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 160 optimal weight:    0.9990
   chunk 171 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0060
   chunk 148 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 177 optimal weight:    0.8980
   chunk 131 optimal weight:    8.9990
   chunk 152 optimal weight:    0.9980
   chunk 134 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.7198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.128090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.089535 restraints weight = 35987.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.092554 restraints weight = 18558.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.094376 restraints weight = 13113.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.095477 restraints weight = 10855.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.096189 restraints weight = 9742.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  15316  Z= 0.122
  Angle     :  0.553  11.800  20740  Z= 0.290
  Chirality :  0.037   0.116   2344
  Planarity :  0.003   0.029   2608
  Dihedral  :  3.614  13.443   2064
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 20.56 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.20), residues: 1872
  helix:  1.95 (0.15), residues: 1372
  sheet:  None (None), residues: 0
  loop : -0.49 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  75 
 TYR   0.014   0.001   TYR G 115 
 PHE   0.044   0.002   PHE C 117 
 TRP   0.011   0.001   TRP G 369 
 HIS   0.003   0.001   HIS G 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (15316)
  covalent geometry    : angle       0.55297 (20740)
  hydrogen bonds       : bond        0.04437 (  977)
  hydrogen bonds       : angle       3.52135 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 244
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A  148 TRP cc_start: 0.6559 (m-10) cc_final: 0.6015 (m100)
REVERT: B   14 LYS cc_start: 0.9094 (tptp) cc_final: 0.8852 (tptp)
REVERT: B  112 ASN cc_start: 0.9024 (m-40) cc_final: 0.8820 (m-40)
REVERT: C  148 TRP cc_start: 0.6556 (m-10) cc_final: 0.6013 (m100)
REVERT: D   14 LYS cc_start: 0.9103 (tptp) cc_final: 0.8861 (tptp)
REVERT: D  112 ASN cc_start: 0.9025 (m-40) cc_final: 0.8820 (m-40)
REVERT: E  148 TRP cc_start: 0.6563 (m-10) cc_final: 0.6018 (m100)
REVERT: F   14 LYS cc_start: 0.9098 (tptp) cc_final: 0.8857 (tptp)
REVERT: F  112 ASN cc_start: 0.9028 (m-40) cc_final: 0.8824 (m-40)
REVERT: G  148 TRP cc_start: 0.6557 (m-10) cc_final: 0.6013 (m100)
REVERT: H   14 LYS cc_start: 0.9096 (tptp) cc_final: 0.8857 (tptp)
REVERT: H  112 ASN cc_start: 0.9025 (m-40) cc_final: 0.8820 (m-40)
  outliers start: 21
  outliers final: 21
  residues processed: 257
  average time/residue: 0.1108
  time to fit residues: 42.7661
Evaluate side-chains
  244 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 223
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  301 THR
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain G residue  105 GLU
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  301 THR
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 183 optimal weight:    7.9990
   chunk 119 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 138 optimal weight:   10.0000
   chunk 141 optimal weight:    6.9990
   chunk 159 optimal weight:    2.9990
   chunk 169 optimal weight:    1.9990
   chunk 152 optimal weight:    2.9990
   chunk 182 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
D 108 HIS
F 108 HIS
H 108 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.127819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.088554 restraints weight = 37982.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.091326 restraints weight = 20119.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.093008 restraints weight = 14409.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.094054 restraints weight = 12003.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.094429 restraints weight = 10807.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029  15316  Z= 0.195
  Angle     :  0.636  11.418  20740  Z= 0.334
  Chirality :  0.040   0.151   2344
  Planarity :  0.003   0.029   2608
  Dihedral  :  3.669  13.363   2064
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 21.67 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.20), residues: 1872
  helix:  1.81 (0.15), residues: 1372
  sheet:  None (None), residues: 0
  loop : -0.53 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  75 
 TYR   0.014   0.002   TYR A 115 
 PHE   0.056   0.002   PHE A 117 
 TRP   0.010   0.001   TRP C 369 
 HIS   0.004   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (15316)
  covalent geometry    : angle       0.63610 (20740)
  hydrogen bonds       : bond        0.05170 (  977)
  hydrogen bonds       : angle       3.78613 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 224
  time to evaluate  : 0.616 
Fit side-chains
REVERT: A  148 TRP cc_start: 0.6586 (m-10) cc_final: 0.6014 (m100)
REVERT: B   14 LYS cc_start: 0.9160 (tptp) cc_final: 0.8928 (tptp)
REVERT: C  148 TRP cc_start: 0.6587 (m-10) cc_final: 0.6016 (m100)
REVERT: D   14 LYS cc_start: 0.9131 (tptp) cc_final: 0.8895 (tptp)
REVERT: E  148 TRP cc_start: 0.6592 (m-10) cc_final: 0.6017 (m100)
REVERT: F   14 LYS cc_start: 0.9157 (tptp) cc_final: 0.8926 (tptp)
REVERT: G  148 TRP cc_start: 0.6589 (m-10) cc_final: 0.6016 (m100)
REVERT: H   14 LYS cc_start: 0.9163 (tptp) cc_final: 0.8930 (tptp)
REVERT: H   42 GLN cc_start: 0.8802 (mm110) cc_final: 0.8468 (mm110)
  outliers start: 30
  outliers final: 30
  residues processed: 248
  average time/residue: 0.1026
  time to fit residues: 38.9160
Evaluate side-chains
  254 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 224
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  301 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue   92 VAL
Chi-restraints excluded: chain G residue   96 ILE
Chi-restraints excluded: chain G residue  105 GLU
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  301 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   92 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 171 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 102 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
D  50 GLN
D 108 HIS
F 108 HIS
H 108 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.126753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.087775 restraints weight = 36594.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.090679 restraints weight = 19078.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.092442 restraints weight = 13592.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.093547 restraints weight = 11296.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.093963 restraints weight = 10161.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15316  Z= 0.148
  Angle     :  0.615  11.845  20740  Z= 0.329
  Chirality :  0.040   0.201   2344
  Planarity :  0.003   0.033   2608
  Dihedral  :  3.626  12.747   2064
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.54 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.20), residues: 1872
  helix:  1.81 (0.15), residues: 1372
  sheet:  None (None), residues: 0
  loop : -0.46 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  75 
 TYR   0.017   0.001   TYR A 115 
 PHE   0.016   0.001   PHE A 113 
 TRP   0.012   0.001   TRP G 369 
 HIS   0.004   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (15316)
  covalent geometry    : angle       0.61469 (20740)
  hydrogen bonds       : bond        0.04866 (  977)
  hydrogen bonds       : angle       3.76307 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 224
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A  148 TRP cc_start: 0.6572 (m-10) cc_final: 0.6016 (m100)
REVERT: A  256 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9199 (mt)
REVERT: B   14 LYS cc_start: 0.9177 (tptp) cc_final: 0.8932 (tptp)
REVERT: C  148 TRP cc_start: 0.6572 (m-10) cc_final: 0.6017 (m100)
REVERT: C  256 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9198 (mt)
REVERT: D   14 LYS cc_start: 0.9184 (tptp) cc_final: 0.8934 (tptp)
REVERT: E  148 TRP cc_start: 0.6574 (m-10) cc_final: 0.6019 (m100)
REVERT: F   14 LYS cc_start: 0.9177 (tptp) cc_final: 0.8932 (tptp)
REVERT: G  148 TRP cc_start: 0.6571 (m-10) cc_final: 0.6016 (m100)
REVERT: H   14 LYS cc_start: 0.9180 (tptp) cc_final: 0.8942 (tptp)
REVERT: H   42 GLN cc_start: 0.8836 (mm110) cc_final: 0.8493 (mm110)
  outliers start: 33
  outliers final: 23
  residues processed: 246
  average time/residue: 0.1082
  time to fit residues: 40.7419
Evaluate side-chains
  249 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 224
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  301 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain G residue   96 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  301 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 147 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 136 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 142 optimal weight:    8.9990
   chunk 176 optimal weight:    0.2980
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
B 112 ASN
D 112 ASN
F 112 ASN
H 112 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.129331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.090282 restraints weight = 36971.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.093013 restraints weight = 19548.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.094750 restraints weight = 13949.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.095619 restraints weight = 11571.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.095927 restraints weight = 10501.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15316  Z= 0.179
  Angle     :  0.654  11.568  20740  Z= 0.348
  Chirality :  0.041   0.173   2344
  Planarity :  0.003   0.032   2608
  Dihedral  :  3.666  12.525   2064
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.00 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.20), residues: 1872
  helix:  1.76 (0.15), residues: 1368
  sheet:  None (None), residues: 0
  loop : -0.56 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  75 
 TYR   0.015   0.001   TYR A 115 
 PHE   0.014   0.001   PHE F  93 
 TRP   0.011   0.001   TRP A 369 
 HIS   0.002   0.001   HIS C 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (15316)
  covalent geometry    : angle       0.65377 (20740)
  hydrogen bonds       : bond        0.05197 (  977)
  hydrogen bonds       : angle       3.87428 ( 2871)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 212
  time to evaluate  : 0.568 
Fit side-chains
REVERT: A  256 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9229 (mt)
REVERT: B   14 LYS cc_start: 0.9146 (tptp) cc_final: 0.8915 (tptp)
REVERT: C  256 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9228 (mt)
REVERT: D   14 LYS cc_start: 0.9147 (tptp) cc_final: 0.8927 (tptp)
REVERT: E  256 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9228 (mt)
REVERT: F   14 LYS cc_start: 0.9139 (tptp) cc_final: 0.8924 (tptp)
REVERT: G  256 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9229 (mt)
REVERT: H   14 LYS cc_start: 0.9148 (tptp) cc_final: 0.8936 (tptp)
  outliers start: 34
  outliers final: 27
  residues processed: 240
  average time/residue: 0.1072
  time to fit residues: 39.2725
Evaluate side-chains
  243 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 212
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  112 ASN
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue  112 ASN
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  153 LEU
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  301 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  112 ASN
Chi-restraints excluded: chain G residue   96 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain G residue  256 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  301 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue  112 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 131 optimal weight:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 144 optimal weight:    0.7980
   chunk 102 optimal weight:    0.6980
   chunk 172 optimal weight:    0.0670
   chunk 157 optimal weight:    0.5980
   chunk 93 optimal weight:    0.0980
   chunk 182 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 177 optimal weight:    7.9990
   overall best weight:    0.4518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.128188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.090274 restraints weight = 36172.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.093285 restraints weight = 18598.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.095133 restraints weight = 13099.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.096218 restraints weight = 10804.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.096891 restraints weight = 9665.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15316  Z= 0.128
  Angle     :  0.631  12.087  20740  Z= 0.334
  Chirality :  0.039   0.180   2344
  Planarity :  0.003   0.031   2608
  Dihedral  :  3.594  13.400   2064
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 22.58 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.21), residues: 1872
  helix:  1.86 (0.15), residues: 1364
  sheet:  None (None), residues: 0
  loop : -0.43 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  75 
 TYR   0.016   0.001   TYR A 115 
 PHE   0.013   0.001   PHE A 113 
 TRP   0.014   0.001   TRP E 369 
 HIS   0.002   0.000   HIS D 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (15316)
  covalent geometry    : angle       0.63102 (20740)
  hydrogen bonds       : bond        0.04405 (  977)
  hydrogen bonds       : angle       3.67863 ( 2871)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2822.75 seconds
wall clock time: 49 minutes 16.47 seconds (2956.47 seconds total)