Starting phenix.real_space_refine
on Thu Jan 23 01:50:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ja0_61286/01_2025/9ja0_61286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ja0_61286/01_2025/9ja0_61286.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ja0_61286/01_2025/9ja0_61286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ja0_61286/01_2025/9ja0_61286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ja0_61286/01_2025/9ja0_61286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ja0_61286/01_2025/9ja0_61286.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.027
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     168      5.16       5
     C   12384      2.51       5
     N    3492      2.21       5
     O    3672      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 19716
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1643
          Classifications: {'peptide': 219}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 16, 'TRANS': 202}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 29
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 5.95, per 1000 atoms: 0.30
  Number of scatterers: 19716
  At special positions: 0
  Unit cell: (106.941, 116.889, 128.495, 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     168     16.00
     O    3672      8.00
     N    3492      7.00
     C   12384      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 198 " - pdb=" SG  CYS A 218 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.37
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4944

  Finding SS restraints...
    Secondary structure from input PDB file:
      144 helices and 12 sheets defined
      67.1% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 30
      removed outlier: 3.584A  pdb=" N   VAL A  27 " --> pdb=" O   TRP A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 44
    Processing helix  chain 'A' and resid 48 through 58
    Processing helix  chain 'A' and resid 62 through 84
      removed outlier: 3.541A  pdb=" N   MET A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 110 through 120
    Processing helix  chain 'A' and resid 125 through 145
      removed outlier: 3.701A  pdb=" N   LYS A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET A 144 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP A 152 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 175
    Processing helix  chain 'A' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU A 187 " --> pdb=" O   ASN A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 204
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 4.165A  pdb=" N   THR A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 30
      removed outlier: 3.584A  pdb=" N   VAL B  27 " --> pdb=" O   TRP B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 44
    Processing helix  chain 'B' and resid 48 through 58
    Processing helix  chain 'B' and resid 62 through 84
      removed outlier: 3.541A  pdb=" N   MET B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 105
    Processing helix  chain 'B' and resid 110 through 120
    Processing helix  chain 'B' and resid 125 through 145
      removed outlier: 3.702A  pdb=" N   LYS B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS B 140 " --> pdb=" O   LEU B 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET B 144 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP B 152 " --> pdb=" O   SER B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 175
    Processing helix  chain 'B' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU B 187 " --> pdb=" O   ASN B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 204
    Processing helix  chain 'B' and resid 210 through 216
      removed outlier: 4.164A  pdb=" N   THR B 216 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 30
      removed outlier: 3.584A  pdb=" N   VAL C  27 " --> pdb=" O   TRP C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 44
    Processing helix  chain 'C' and resid 48 through 58
    Processing helix  chain 'C' and resid 62 through 84
      removed outlier: 3.540A  pdb=" N   MET C  68 " --> pdb=" O   ALA C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 105
    Processing helix  chain 'C' and resid 110 through 120
    Processing helix  chain 'C' and resid 125 through 145
      removed outlier: 3.701A  pdb=" N   LYS C 131 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS C 140 " --> pdb=" O   LEU C 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET C 144 " --> pdb=" O   LYS C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP C 152 " --> pdb=" O   SER C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 175
    Processing helix  chain 'C' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU C 187 " --> pdb=" O   ASN C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 204
    Processing helix  chain 'C' and resid 210 through 216
      removed outlier: 4.165A  pdb=" N   THR C 216 " --> pdb=" O   GLU C 212 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 30
      removed outlier: 3.584A  pdb=" N   VAL D  27 " --> pdb=" O   TRP D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 44
    Processing helix  chain 'D' and resid 48 through 58
    Processing helix  chain 'D' and resid 62 through 84
      removed outlier: 3.540A  pdb=" N   MET D  68 " --> pdb=" O   ALA D  64 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 105
    Processing helix  chain 'D' and resid 110 through 120
    Processing helix  chain 'D' and resid 125 through 145
      removed outlier: 3.702A  pdb=" N   LYS D 131 " --> pdb=" O   GLY D 127 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS D 140 " --> pdb=" O   LEU D 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET D 144 " --> pdb=" O   LYS D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 153
      removed outlier: 3.511A  pdb=" N   ASP D 152 " --> pdb=" O   SER D 149 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 175
    Processing helix  chain 'D' and resid 178 through 189
      removed outlier: 3.659A  pdb=" N   GLU D 187 " --> pdb=" O   ASN D 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 204
    Processing helix  chain 'D' and resid 210 through 216
      removed outlier: 4.164A  pdb=" N   THR D 216 " --> pdb=" O   GLU D 212 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 16 through 30
      removed outlier: 3.583A  pdb=" N   VAL E  27 " --> pdb=" O   TRP E  23 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 44
    Processing helix  chain 'E' and resid 48 through 58
    Processing helix  chain 'E' and resid 62 through 84
      removed outlier: 3.540A  pdb=" N   MET E  68 " --> pdb=" O   ALA E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 100 through 105
    Processing helix  chain 'E' and resid 110 through 120
    Processing helix  chain 'E' and resid 125 through 145
      removed outlier: 3.702A  pdb=" N   LYS E 131 " --> pdb=" O   GLY E 127 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS E 140 " --> pdb=" O   LEU E 136 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET E 144 " --> pdb=" O   LYS E 140 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP E 152 " --> pdb=" O   SER E 149 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 175
    Processing helix  chain 'E' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU E 187 " --> pdb=" O   ASN E 183 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 204
    Processing helix  chain 'E' and resid 210 through 216
      removed outlier: 4.165A  pdb=" N   THR E 216 " --> pdb=" O   GLU E 212 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 16 through 30
      removed outlier: 3.584A  pdb=" N   VAL F  27 " --> pdb=" O   TRP F  23 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 44
    Processing helix  chain 'F' and resid 48 through 58
    Processing helix  chain 'F' and resid 62 through 84
      removed outlier: 3.541A  pdb=" N   MET F  68 " --> pdb=" O   ALA F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 105
    Processing helix  chain 'F' and resid 110 through 120
    Processing helix  chain 'F' and resid 125 through 145
      removed outlier: 3.701A  pdb=" N   LYS F 131 " --> pdb=" O   GLY F 127 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS F 140 " --> pdb=" O   LEU F 136 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET F 144 " --> pdb=" O   LYS F 140 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP F 152 " --> pdb=" O   SER F 149 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 160 through 175
    Processing helix  chain 'F' and resid 178 through 189
      removed outlier: 3.659A  pdb=" N   GLU F 187 " --> pdb=" O   ASN F 183 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 195 through 204
    Processing helix  chain 'F' and resid 210 through 216
      removed outlier: 4.164A  pdb=" N   THR F 216 " --> pdb=" O   GLU F 212 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 30
      removed outlier: 3.583A  pdb=" N   VAL G  27 " --> pdb=" O   TRP G  23 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 35 through 44
    Processing helix  chain 'G' and resid 48 through 58
    Processing helix  chain 'G' and resid 62 through 84
      removed outlier: 3.541A  pdb=" N   MET G  68 " --> pdb=" O   ALA G  64 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 100 through 105
    Processing helix  chain 'G' and resid 110 through 120
    Processing helix  chain 'G' and resid 125 through 145
      removed outlier: 3.701A  pdb=" N   LYS G 131 " --> pdb=" O   GLY G 127 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS G 140 " --> pdb=" O   LEU G 136 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET G 144 " --> pdb=" O   LYS G 140 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP G 152 " --> pdb=" O   SER G 149 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 160 through 175
    Processing helix  chain 'G' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU G 187 " --> pdb=" O   ASN G 183 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 195 through 204
    Processing helix  chain 'G' and resid 210 through 216
      removed outlier: 4.165A  pdb=" N   THR G 216 " --> pdb=" O   GLU G 212 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 16 through 30
      removed outlier: 3.584A  pdb=" N   VAL H  27 " --> pdb=" O   TRP H  23 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 35 through 44
    Processing helix  chain 'H' and resid 48 through 58
    Processing helix  chain 'H' and resid 62 through 84
      removed outlier: 3.541A  pdb=" N   MET H  68 " --> pdb=" O   ALA H  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 105
    Processing helix  chain 'H' and resid 110 through 120
    Processing helix  chain 'H' and resid 125 through 145
      removed outlier: 3.702A  pdb=" N   LYS H 131 " --> pdb=" O   GLY H 127 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS H 140 " --> pdb=" O   LEU H 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET H 144 " --> pdb=" O   LYS H 140 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP H 152 " --> pdb=" O   SER H 149 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 160 through 175
    Processing helix  chain 'H' and resid 178 through 189
      removed outlier: 3.659A  pdb=" N   GLU H 187 " --> pdb=" O   ASN H 183 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 195 through 204
    Processing helix  chain 'H' and resid 210 through 216
      removed outlier: 4.164A  pdb=" N   THR H 216 " --> pdb=" O   GLU H 212 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 16 through 30
      removed outlier: 3.583A  pdb=" N   VAL I  27 " --> pdb=" O   TRP I  23 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 35 through 44
    Processing helix  chain 'I' and resid 48 through 58
    Processing helix  chain 'I' and resid 62 through 84
      removed outlier: 3.541A  pdb=" N   MET I  68 " --> pdb=" O   ALA I  64 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 105
    Processing helix  chain 'I' and resid 110 through 120
    Processing helix  chain 'I' and resid 125 through 145
      removed outlier: 3.701A  pdb=" N   LYS I 131 " --> pdb=" O   GLY I 127 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS I 140 " --> pdb=" O   LEU I 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET I 144 " --> pdb=" O   LYS I 140 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 149 through 153
      removed outlier: 3.511A  pdb=" N   ASP I 152 " --> pdb=" O   SER I 149 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 160 through 175
    Processing helix  chain 'I' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU I 187 " --> pdb=" O   ASN I 183 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 195 through 204
    Processing helix  chain 'I' and resid 210 through 216
      removed outlier: 4.164A  pdb=" N   THR I 216 " --> pdb=" O   GLU I 212 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 16 through 30
      removed outlier: 3.583A  pdb=" N   VAL J  27 " --> pdb=" O   TRP J  23 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 35 through 44
    Processing helix  chain 'J' and resid 48 through 58
    Processing helix  chain 'J' and resid 62 through 84
      removed outlier: 3.542A  pdb=" N   MET J  68 " --> pdb=" O   ALA J  64 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 100 through 105
    Processing helix  chain 'J' and resid 110 through 120
    Processing helix  chain 'J' and resid 125 through 145
      removed outlier: 3.701A  pdb=" N   LYS J 131 " --> pdb=" O   GLY J 127 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS J 140 " --> pdb=" O   LEU J 136 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET J 144 " --> pdb=" O   LYS J 140 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP J 152 " --> pdb=" O   SER J 149 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 160 through 175
    Processing helix  chain 'J' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU J 187 " --> pdb=" O   ASN J 183 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 195 through 204
    Processing helix  chain 'J' and resid 210 through 216
      removed outlier: 4.164A  pdb=" N   THR J 216 " --> pdb=" O   GLU J 212 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 16 through 30
      removed outlier: 3.584A  pdb=" N   VAL K  27 " --> pdb=" O   TRP K  23 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 35 through 44
    Processing helix  chain 'K' and resid 48 through 58
    Processing helix  chain 'K' and resid 62 through 84
      removed outlier: 3.541A  pdb=" N   MET K  68 " --> pdb=" O   ALA K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 100 through 105
    Processing helix  chain 'K' and resid 110 through 120
    Processing helix  chain 'K' and resid 125 through 145
      removed outlier: 3.702A  pdb=" N   LYS K 131 " --> pdb=" O   GLY K 127 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS K 140 " --> pdb=" O   LEU K 136 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET K 144 " --> pdb=" O   LYS K 140 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 149 through 153
      removed outlier: 3.511A  pdb=" N   ASP K 152 " --> pdb=" O   SER K 149 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 160 through 175
    Processing helix  chain 'K' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU K 187 " --> pdb=" O   ASN K 183 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 195 through 204
    Processing helix  chain 'K' and resid 210 through 216
      removed outlier: 4.164A  pdb=" N   THR K 216 " --> pdb=" O   GLU K 212 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 16 through 30
      removed outlier: 3.583A  pdb=" N   VAL L  27 " --> pdb=" O   TRP L  23 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 35 through 44
    Processing helix  chain 'L' and resid 48 through 58
    Processing helix  chain 'L' and resid 62 through 84
      removed outlier: 3.540A  pdb=" N   MET L  68 " --> pdb=" O   ALA L  64 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 100 through 105
    Processing helix  chain 'L' and resid 110 through 120
    Processing helix  chain 'L' and resid 125 through 145
      removed outlier: 3.701A  pdb=" N   LYS L 131 " --> pdb=" O   GLY L 127 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS L 140 " --> pdb=" O   LEU L 136 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET L 144 " --> pdb=" O   LYS L 140 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 149 through 153
      removed outlier: 3.510A  pdb=" N   ASP L 152 " --> pdb=" O   SER L 149 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 160 through 175
    Processing helix  chain 'L' and resid 178 through 189
      removed outlier: 3.660A  pdb=" N   GLU L 187 " --> pdb=" O   ASN L 183 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 195 through 204
    Processing helix  chain 'L' and resid 210 through 216
      removed outlier: 4.165A  pdb=" N   THR L 216 " --> pdb=" O   GLU L 212 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4
    Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4
    Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4
    Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4
    Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4
    Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 4
    Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 4
    Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 4
    Processing sheet with id=AB1, first strand: chain 'J' and resid 2 through 4
    Processing sheet with id=AB2, first strand: chain 'K' and resid 2 through 4
    Processing sheet with id=AB3, first strand: chain 'L' and resid 2 through 4

    1128 hydrogen bonds defined for protein.
    3348 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: 6.13

  Time building geometry restraints manager: 5.06 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: 6673
        1.34 -     1.46: 3267
        1.46 -     1.58: 9860
        1.58 -     1.69: 0
        1.69 -     1.81: 288
  Bond restraints: 20088
  Sorted by residual:
  bond pdb=" C   ILE G  37 "
       pdb=" O   ILE G  37 "
    ideal  model  delta    sigma   weight residual
    1.242  1.227  0.015 8.60e-03 1.35e+04 2.92e+00
  bond pdb=" C   ILE E  37 "
       pdb=" O   ILE E  37 "
    ideal  model  delta    sigma   weight residual
    1.242  1.227  0.015 8.60e-03 1.35e+04 2.87e+00
  bond pdb=" C   ILE L  37 "
       pdb=" O   ILE L  37 "
    ideal  model  delta    sigma   weight residual
    1.242  1.227  0.015 8.60e-03 1.35e+04 2.87e+00
  bond pdb=" C   ILE C  37 "
       pdb=" O   ILE C  37 "
    ideal  model  delta    sigma   weight residual
    1.242  1.227  0.015 8.60e-03 1.35e+04 2.87e+00
  bond pdb=" C   ILE D  37 "
       pdb=" O   ILE D  37 "
    ideal  model  delta    sigma   weight residual
    1.242  1.228  0.014 8.60e-03 1.35e+04 2.74e+00
  ... (remaining 20083 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 26098
        1.40 -     2.80: 972
        2.80 -     4.20: 194
        4.20 -     5.60: 36
        5.60 -     7.01: 24
  Bond angle restraints: 27324
  Sorted by residual:
  angle pdb=" N   PRO I 122 "
        pdb=" CA  PRO I 122 "
        pdb=" C   PRO I 122 "
      ideal   model   delta    sigma   weight residual
     110.70  103.69    7.01 1.22e+00 6.72e-01 3.30e+01
  angle pdb=" N   PRO G 122 "
        pdb=" CA  PRO G 122 "
        pdb=" C   PRO G 122 "
      ideal   model   delta    sigma   weight residual
     110.70  103.70    7.00 1.22e+00 6.72e-01 3.29e+01
  angle pdb=" N   PRO L 122 "
        pdb=" CA  PRO L 122 "
        pdb=" C   PRO L 122 "
      ideal   model   delta    sigma   weight residual
     110.70  103.71    6.99 1.22e+00 6.72e-01 3.29e+01
  angle pdb=" N   PRO C 122 "
        pdb=" CA  PRO C 122 "
        pdb=" C   PRO C 122 "
      ideal   model   delta    sigma   weight residual
     110.70  103.71    6.99 1.22e+00 6.72e-01 3.29e+01
  angle pdb=" N   PRO D 122 "
        pdb=" CA  PRO D 122 "
        pdb=" C   PRO D 122 "
      ideal   model   delta    sigma   weight residual
     110.70  103.73    6.97 1.22e+00 6.72e-01 3.27e+01
  ... (remaining 27319 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.78: 10995
       13.78 -    27.56: 971
       27.56 -    41.34: 205
       41.34 -    55.12: 72
       55.12 -    68.90: 24
  Dihedral angle restraints: 12267
    sinusoidal: 4659
      harmonic: 7608
  Sorted by residual:
  dihedral pdb=" CG  ARG F 143 "
           pdb=" CD  ARG F 143 "
           pdb=" NE  ARG F 143 "
           pdb=" CZ  ARG F 143 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.07   41.93     2      1.50e+01 4.44e-03 9.53e+00
  dihedral pdb=" CG  ARG C 143 "
           pdb=" CD  ARG C 143 "
           pdb=" NE  ARG C 143 "
           pdb=" CZ  ARG C 143 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.09   41.91     2      1.50e+01 4.44e-03 9.52e+00
  dihedral pdb=" CG  ARG E 143 "
           pdb=" CD  ARG E 143 "
           pdb=" NE  ARG E 143 "
           pdb=" CZ  ARG E 143 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  138.11   41.89     2      1.50e+01 4.44e-03 9.51e+00
  ... (remaining 12264 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 2057
       0.035 -    0.070: 805
       0.070 -    0.105: 209
       0.105 -    0.140: 61
       0.140 -    0.174: 36
  Chirality restraints: 3168
  Sorted by residual:
  chirality pdb=" CA  ILE C 124 "
            pdb=" N   ILE C 124 "
            pdb=" C   ILE C 124 "
            pdb=" CB  ILE C 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.61e-01
  chirality pdb=" CA  ILE F 124 "
            pdb=" N   ILE F 124 "
            pdb=" C   ILE F 124 "
            pdb=" CB  ILE F 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CA  ILE A 124 "
            pdb=" N   ILE A 124 "
            pdb=" C   ILE A 124 "
            pdb=" CB  ILE A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.41e-01
  ... (remaining 3165 not shown)

  Planarity restraints: 3552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G  48 "    0.032 5.00e-02 4.00e+02   4.86e-02 3.77e+00
        pdb=" N   PRO G  49 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  48 "   -0.032 5.00e-02 4.00e+02   4.85e-02 3.77e+00
        pdb=" N   PRO C  49 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR J  48 "   -0.032 5.00e-02 4.00e+02   4.85e-02 3.77e+00
        pdb=" N   PRO J  49 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO J  49 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO J  49 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 3549 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 130
        2.55 -     3.14: 14979
        3.14 -     3.72: 30098
        3.72 -     4.31: 42841
        4.31 -     4.90: 68325
  Nonbonded interactions: 156373
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A  14 "
            pdb=" SG  CYS B  45 "
     model   vdw
     1.961 3.760
  nonbonded pdb=" SG  CYS E  14 "
            pdb=" SG  CYS F  45 "
     model   vdw
     1.997 3.760
  nonbonded pdb=" SG  CYS H  45 "
            pdb=" SG  CYS I  14 "
     model   vdw
     2.000 3.760
  nonbonded pdb=" SG  CYS D  45 "
            pdb=" SG  CYS F  14 "
     model   vdw
     2.000 3.760
  nonbonded pdb=" SG  CYS C  45 "
            pdb=" SG  CYS D  14 "
     model   vdw
     2.006 3.760
  ... (remaining 156368 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: 0.19
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.680
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     36.840
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
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   0.035  20088  Z= 0.223
  Angle     :  0.668   7.005  27324  Z= 0.438
  Chirality :  0.044   0.174   3168
  Planarity :  0.006   0.049   3552
  Dihedral  : 11.921  68.899   7320
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.28 (0.12), residues: 2604
  helix: -3.25 (0.08), residues: 1620
  sheet:  None (None), residues: 0
  loop : -1.74 (0.17), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 117 
 HIS   0.002   0.001   HIS F  12 
 PHE   0.015   0.002   PHE B  32 
 TYR   0.006   0.001   TYR C 130 
 ARG   0.003   0.001   ARG F 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 363
  time to evaluate  : 2.091 
Fit side-chains
REVERT: A  112 GLN cc_start: 0.7809 (mp-120) cc_final: 0.7564 (mp10)
REVERT: C    4 GLN cc_start: 0.7971 (tt0) cc_final: 0.7351 (tm-30)
REVERT: D  112 GLN cc_start: 0.7773 (mp-120) cc_final: 0.7489 (mp-120)
REVERT: E    4 GLN cc_start: 0.7976 (tt0) cc_final: 0.7334 (tm-30)
REVERT: F  112 GLN cc_start: 0.7727 (mp-120) cc_final: 0.7444 (mp10)
REVERT: H  112 GLN cc_start: 0.7712 (mp-120) cc_final: 0.7432 (mp10)
REVERT: J   39 MET cc_start: 0.8717 (tpt) cc_final: 0.8516 (tpp)
REVERT: J  112 GLN cc_start: 0.7777 (mp-120) cc_final: 0.7490 (mp-120)
REVERT: K  112 GLN cc_start: 0.7742 (mp-120) cc_final: 0.7469 (mp10)
REVERT: L    4 GLN cc_start: 0.7971 (tt0) cc_final: 0.7339 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 363
  average time/residue: 0.3044
  time to fit residues: 171.0142
Evaluate side-chains
  280 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 2.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 212 optimal weight:    2.9990
   chunk 191 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 102 optimal weight:    9.9990
   chunk 197 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 120 optimal weight:    5.9990
   chunk 147 optimal weight:    0.0570
   chunk 228 optimal weight:    8.9990
   overall best weight:    1.5704

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
A 193 ASN
B   4 GLN
B 193 ASN
C 112 GLN
C 193 ASN
D   4 GLN
D 193 ASN
E 193 ASN
F   4 GLN
F 193 ASN
G   4 GLN
G 193 ASN
H   4 GLN
H 193 ASN
I   4 GLN
I 193 ASN
J   4 GLN
J 193 ASN
K   4 GLN
K 193 ASN
L 193 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.184182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.130117 restraints weight = 20723.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.66
r_work: 0.3334 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  20088  Z= 0.294
  Angle     :  0.563   5.795  27324  Z= 0.295
  Chirality :  0.045   0.129   3168
  Planarity :  0.005   0.039   3552
  Dihedral  :  4.207  19.207   2784
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.34 %
    Favored  : 91.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.15), residues: 2604
  helix: -0.87 (0.11), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.52 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP F 117 
 HIS   0.003   0.001   HIS G  84 
 PHE   0.014   0.002   PHE A  32 
 TYR   0.014   0.002   TYR B 130 
 ARG   0.002   0.001   ARG D 167 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 303
  time to evaluate  : 2.140 
Fit side-chains
REVERT: A   33 SER cc_start: 0.8919 (m) cc_final: 0.8629 (t)
REVERT: B   82 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7143 (ttp80)
REVERT: C   82 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7169 (ttp80)
REVERT: D   82 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7140 (ttp80)
REVERT: G   82 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7138 (ttp80)
REVERT: J   82 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7147 (ttp80)
  outliers start: 15
  outliers final: 12
  residues processed: 309
  average time/residue: 0.3219
  time to fit residues: 151.4435
Evaluate side-chains
  311 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 299
  time to evaluate  : 2.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  136 LEU
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain H residue  136 LEU
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain J residue   11 VAL
Chi-restraints excluded: chain L residue   11 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 146 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9980
   chunk 133 optimal weight:    1.9990
   chunk 231 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 151 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0670
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
C   4 GLN
E   4 GLN
F   4 GLN
H   4 GLN
K   4 GLN
L   4 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.187581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.133607 restraints weight = 20438.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.66
r_work: 0.3369 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  20088  Z= 0.156
  Angle     :  0.455   5.473  27324  Z= 0.232
  Chirality :  0.041   0.134   3168
  Planarity :  0.005   0.038   3552
  Dihedral  :  3.944  18.924   2784
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.33 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.16), residues: 2604
  helix:  0.32 (0.12), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.45 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  23 
 HIS   0.001   0.000   HIS I  84 
 PHE   0.010   0.002   PHE H  32 
 TYR   0.009   0.001   TYR D 169 
 ARG   0.006   0.000   ARG A 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 277
  time to evaluate  : 2.055 
Fit side-chains
REVERT: C   82 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7120 (ttp80)
REVERT: E   82 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7261 (ttp80)
REVERT: I   82 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7278 (ttp80)
REVERT: L   82 ARG cc_start: 0.7286 (ttp80) cc_final: 0.7078 (ttp80)
  outliers start: 21
  outliers final: 18
  residues processed: 288
  average time/residue: 0.3307
  time to fit residues: 144.0906
Evaluate side-chains
  281 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 263
  time to evaluate  : 2.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue  102 SER
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain E residue  102 SER
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue  102 SER
Chi-restraints excluded: chain F residue  144 MET
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  102 SER
Chi-restraints excluded: chain I residue  102 SER
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue  102 SER
Chi-restraints excluded: chain L residue  102 SER
Chi-restraints excluded: chain L residue  144 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 222 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 251 optimal weight:    4.9990
   chunk 123 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 210 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 194 optimal weight:    0.7980
   chunk 179 optimal weight:    0.6980
   chunk 78 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
C   4 GLN
E   4 GLN
F   4 GLN
H   4 GLN
K   4 GLN
L   4 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.188052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.135390 restraints weight = 20515.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.56
r_work: 0.3369 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  20088  Z= 0.177
  Angle     :  0.439   4.442  27324  Z= 0.223
  Chirality :  0.042   0.129   3168
  Planarity :  0.004   0.039   3552
  Dihedral  :  3.911  19.399   2784
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.03 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.16), residues: 2604
  helix:  0.93 (0.13), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.36 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  23 
 HIS   0.002   0.001   HIS D  84 
 PHE   0.012   0.002   PHE A  32 
 TYR   0.009   0.001   TYR A 169 
 ARG   0.007   0.000   ARG A 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 276
  time to evaluate  : 2.096 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8610 (m-30) cc_final: 0.8316 (m-30)
REVERT: E  103 ASP cc_start: 0.8585 (m-30) cc_final: 0.8275 (m-30)
REVERT: I  103 ASP cc_start: 0.8566 (m-30) cc_final: 0.8252 (m-30)
REVERT: L   82 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7132 (ttp80)
REVERT: L  103 ASP cc_start: 0.8602 (m-30) cc_final: 0.8298 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 280
  average time/residue: 0.3297
  time to fit residues: 139.2499
Evaluate side-chains
  285 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 273
  time to evaluate  : 2.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain F residue  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain J residue  144 MET
Chi-restraints excluded: chain K residue  144 MET
Chi-restraints excluded: chain L residue  144 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 121 optimal weight:    0.7980
   chunk 138 optimal weight:    0.9980
   chunk 211 optimal weight:    4.9990
   chunk 137 optimal weight:    0.8980
   chunk 113 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 158 optimal weight:    2.9990
   chunk 243 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
C   4 GLN
E   4 GLN
F   4 GLN
H   4 GLN
I   4 GLN
K   4 GLN
L   4 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.184139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.130735 restraints weight = 20718.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.57
r_work: 0.3316 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  20088  Z= 0.280
  Angle     :  0.485   4.521  27324  Z= 0.246
  Chirality :  0.044   0.136   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  4.085  19.950   2784
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.03 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.16), residues: 2604
  helix:  1.00 (0.13), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.37 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP I  80 
 HIS   0.002   0.001   HIS G  84 
 PHE   0.013   0.002   PHE A  32 
 TYR   0.008   0.002   TYR A 169 
 ARG   0.005   0.001   ARG A 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 271
  time to evaluate  : 2.128 
Fit side-chains
REVERT: L   82 ARG cc_start: 0.7440 (ttp80) cc_final: 0.7166 (ttp80)
  outliers start: 22
  outliers final: 22
  residues processed: 278
  average time/residue: 0.3367
  time to fit residues: 141.1331
Evaluate side-chains
  283 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 261
  time to evaluate  : 2.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue  136 LEU
Chi-restraints excluded: chain F residue  144 MET
Chi-restraints excluded: chain G residue  102 SER
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  136 LEU
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain J residue  102 SER
Chi-restraints excluded: chain J residue  144 MET
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue  136 LEU
Chi-restraints excluded: chain K residue  144 MET
Chi-restraints excluded: chain L residue  144 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0170
   chunk 213 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0050
   chunk 86 optimal weight:    0.9980
   chunk 239 optimal weight:    0.0010
   chunk 5 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
K   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.188516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.135943 restraints weight = 20362.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.56
r_work: 0.3386 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  20088  Z= 0.125
  Angle     :  0.409   4.309  27324  Z= 0.207
  Chirality :  0.041   0.128   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.832  19.730   2784
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.93 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.17), residues: 2604
  helix:  1.40 (0.13), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.31 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  23 
 HIS   0.001   0.000   HIS K  12 
 PHE   0.009   0.001   PHE H  32 
 TYR   0.010   0.001   TYR A 169 
 ARG   0.008   0.000   ARG A 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 290
  time to evaluate  : 2.220 
Fit side-chains
REVERT: C   82 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7262 (ttp80)
REVERT: C  103 ASP cc_start: 0.8544 (m-30) cc_final: 0.8341 (m-30)
REVERT: I  103 ASP cc_start: 0.8535 (m-30) cc_final: 0.8158 (m-30)
REVERT: L   82 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7196 (ttp80)
REVERT: L  103 ASP cc_start: 0.8507 (m-30) cc_final: 0.8283 (m-30)
  outliers start: 20
  outliers final: 14
  residues processed: 294
  average time/residue: 0.3637
  time to fit residues: 157.2649
Evaluate side-chains
  285 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 271
  time to evaluate  : 2.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain D residue  102 SER
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain J residue  144 MET
Chi-restraints excluded: chain K residue  144 MET
Chi-restraints excluded: chain L residue  144 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 192 optimal weight:    0.0020
   chunk 197 optimal weight:    0.3980
   chunk 41 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 191 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 134 optimal weight:    0.0870
   chunk 182 optimal weight:    0.2980
   chunk 154 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 247 optimal weight:    0.8980
   overall best weight:    0.2966

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
F   4 GLN
H   4 GLN
K   4 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.189628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.137634 restraints weight = 20224.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.54
r_work: 0.3403 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  20088  Z= 0.117
  Angle     :  0.403   4.339  27324  Z= 0.203
  Chirality :  0.040   0.126   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.726  19.739   2784
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 12.03 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.17), residues: 2604
  helix:  1.63 (0.13), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.27 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  23 
 HIS   0.001   0.000   HIS L  84 
 PHE   0.010   0.001   PHE A  32 
 TYR   0.009   0.001   TYR A 169 
 ARG   0.007   0.000   ARG F 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 293
  time to evaluate  : 2.266 
Fit side-chains
REVERT: C   82 ARG cc_start: 0.7499 (ttp80) cc_final: 0.7204 (ttp80)
REVERT: C  103 ASP cc_start: 0.8529 (m-30) cc_final: 0.8306 (m-30)
REVERT: C  154 ARG cc_start: 0.7597 (mtt-85) cc_final: 0.7299 (mtt-85)
REVERT: E  154 ARG cc_start: 0.7618 (mtt-85) cc_final: 0.7325 (mtt-85)
REVERT: I  154 ARG cc_start: 0.7612 (mtt-85) cc_final: 0.7318 (mtt-85)
REVERT: J   25 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8084 (mmmt)
REVERT: L   82 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7221 (ttp80)
REVERT: L  103 ASP cc_start: 0.8540 (m-30) cc_final: 0.8324 (m-30)
REVERT: L  154 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7301 (mtt-85)
  outliers start: 19
  outliers final: 13
  residues processed: 296
  average time/residue: 0.3520
  time to fit residues: 154.1556
Evaluate side-chains
  294 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 281
  time to evaluate  : 2.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 MET
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain F residue  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain J residue  144 MET
Chi-restraints excluded: chain K residue  144 MET
Chi-restraints excluded: chain L residue  144 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 250 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 211 optimal weight:    0.5980
   chunk 17 optimal weight:   10.0000
   chunk 110 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 157 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 116 optimal weight:    0.8980
   chunk 225 optimal weight:    2.9990
   chunk 216 optimal weight:    4.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
C   4 GLN
F   4 GLN
H   4 GLN
K   4 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.185179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.132038 restraints weight = 20460.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.57
r_work: 0.3331 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  20088  Z= 0.219
  Angle     :  0.454   4.507  27324  Z= 0.229
  Chirality :  0.043   0.135   3168
  Planarity :  0.004   0.039   3552
  Dihedral  :  3.900  19.265   2784
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 12.18 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.17), residues: 2604
  helix:  1.47 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.23 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J  23 
 HIS   0.002   0.001   HIS D  84 
 PHE   0.013   0.002   PHE H  32 
 TYR   0.008   0.001   TYR A 169 
 ARG   0.007   0.001   ARG A 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 277
  time to evaluate  : 2.213 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8494 (m-30) cc_final: 0.8275 (m-30)
REVERT: E  103 ASP cc_start: 0.8567 (m-30) cc_final: 0.8253 (m-30)
REVERT: L   82 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7277 (ttp80)
REVERT: L  103 ASP cc_start: 0.8518 (m-30) cc_final: 0.8308 (m-30)
  outliers start: 18
  outliers final: 17
  residues processed: 279
  average time/residue: 0.3711
  time to fit residues: 151.2674
Evaluate side-chains
  290 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 273
  time to evaluate  : 2.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue  136 LEU
Chi-restraints excluded: chain F residue  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  136 LEU
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain J residue  144 MET
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue  144 MET
Chi-restraints excluded: chain L residue  144 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 135 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 197 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 216 optimal weight:    0.9990
   chunk 215 optimal weight:    0.8980
   chunk 220 optimal weight:    2.9990
   chunk 166 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0270
   chunk 133 optimal weight:    1.9990
   overall best weight:    0.7640

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
F   4 GLN
H   4 GLN
K   4 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.186601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.133774 restraints weight = 20337.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.57
r_work: 0.3352 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  20088  Z= 0.164
  Angle     :  0.430   4.402  27324  Z= 0.217
  Chirality :  0.042   0.130   3168
  Planarity :  0.005   0.038   3552
  Dihedral  :  3.821  19.603   2784
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.67 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.17), residues: 2604
  helix:  1.62 (0.13), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.19 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J  23 
 HIS   0.001   0.000   HIS K  84 
 PHE   0.010   0.001   PHE H  32 
 TYR   0.009   0.001   TYR I 169 
 ARG   0.009   0.001   ARG I 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 284
  time to evaluate  : 2.130 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8524 (m-30) cc_final: 0.8308 (m-30)
REVERT: E  103 ASP cc_start: 0.8559 (m-30) cc_final: 0.8242 (m-30)
REVERT: G  154 ARG cc_start: 0.7719 (mtt-85) cc_final: 0.7370 (mtt-85)
REVERT: L   82 ARG cc_start: 0.7582 (ttp80) cc_final: 0.7262 (ttp80)
REVERT: L  103 ASP cc_start: 0.8511 (m-30) cc_final: 0.8296 (m-30)
  outliers start: 20
  outliers final: 14
  residues processed: 286
  average time/residue: 0.3630
  time to fit residues: 152.5164
Evaluate side-chains
  295 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 281
  time to evaluate  : 2.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 MET
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain F residue  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain J residue  144 MET
Chi-restraints excluded: chain K residue  144 MET
Chi-restraints excluded: chain L residue  144 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 127 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 116 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 200 optimal weight:    0.6980
   chunk 155 optimal weight:    0.8980
   chunk 126 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 206 optimal weight:    6.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
F   4 GLN
H   4 GLN
K   4 GLN
L   4 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.186259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.132463 restraints weight = 20327.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.63
r_work: 0.3342 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  20088  Z= 0.174
  Angle     :  0.434   4.447  27324  Z= 0.218
  Chirality :  0.042   0.130   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.832  19.564   2784
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.82 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.17), residues: 2604
  helix:  1.63 (0.13), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.19 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP J  23 
 HIS   0.002   0.000   HIS C  84 
 PHE   0.011   0.002   PHE H  32 
 TYR   0.009   0.001   TYR I 169 
 ARG   0.007   0.000   ARG A 154 

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

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

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5208 Ramachandran restraints generated.
    2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 279
  time to evaluate  : 2.220 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8493 (m-30) cc_final: 0.8283 (m-30)
REVERT: E  103 ASP cc_start: 0.8560 (m-30) cc_final: 0.8254 (m-30)
REVERT: J   25 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8148 (mmmt)
REVERT: L   82 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7270 (ttp80)
REVERT: L  103 ASP cc_start: 0.8502 (m-30) cc_final: 0.8286 (m-30)
  outliers start: 13
  outliers final: 13
  residues processed: 279
  average time/residue: 0.3718
  time to fit residues: 150.8231
Evaluate side-chains
  291 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 278
  time to evaluate  : 2.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain D residue  144 MET
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain F residue  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain J residue  144 MET
Chi-restraints excluded: chain K residue  144 MET
Chi-restraints excluded: chain L residue  144 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 79 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 189 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 190 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 180 optimal weight:    0.3980
   chunk 103 optimal weight:    9.9990
   chunk 89 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
E   4 GLN
F   4 GLN
H   4 GLN
K   4 GLN
L   4 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.186752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.133068 restraints weight = 20474.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 2.63
r_work: 0.3351 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  20088  Z= 0.162
  Angle     :  0.429   4.440  27324  Z= 0.216
  Chirality :  0.042   0.129   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.809  19.645   2784
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.02 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.17), residues: 2604
  helix:  1.69 (0.13), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.18 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  23 
 HIS   0.001   0.000   HIS D  84 
 PHE   0.010   0.001   PHE H  32 
 TYR   0.009   0.001   TYR I 169 
 ARG   0.007   0.000   ARG A 154 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8233.92 seconds
wall clock time: 147 minutes 5.54 seconds (8825.54 seconds total)