Starting phenix.real_space_refine
on Tue May 20 04:23:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ja0_61286/05_2025/9ja0_61286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ja0_61286/05_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_61286/05_2025/9ja0_61286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ja0_61286/05_2025/9ja0_61286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ja0_61286/05_2025/9ja0_61286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ja0_61286/05_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-5687/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: 5.47, per 1000 atoms: 0.28
  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=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  14 " - pdb=" SG  CYS B  45 " distance=1.96
    Simple disulfide: pdb=" SG  CYS A  45 " - pdb=" SG  CYS C  14 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 198 " - pdb=" SG  CYS A 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  14 " - pdb=" SG  CYS E  45 " distance=2.01
    Simple disulfide: pdb=" SG  CYS E  14 " - pdb=" SG  CYS F  45 " distance=2.00
    Simple disulfide: pdb=" SG  CYS D  14 " - pdb=" SG  CYS C  45 " distance=2.01
    Simple disulfide: pdb=" SG  CYS G  14 " - pdb=" SG  CYS L  45 " distance=2.01
    Simple disulfide: pdb=" SG  CYS F  14 " - pdb=" SG  CYS D  45 " distance=2.00
    Simple disulfide: pdb=" SG  CYS I  14 " - pdb=" SG  CYS H  45 " distance=2.00
    Simple disulfide: pdb=" SG  CYS H  14 " - pdb=" SG  CYS G  45 " distance=2.01
    Simple disulfide: pdb=" SG  CYS K  14 " - pdb=" SG  CYS J  45 " distance=2.01
    Simple disulfide: pdb=" SG  CYS J  14 " - pdb=" SG  CYS I  45 " distance=2.01
    Simple disulfide: pdb=" SG  CYS L  14 " - pdb=" SG  CYS K  45 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 198 " - pdb=" SG  CYS C 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 198 " - pdb=" SG  CYS B 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 198 " - pdb=" SG  CYS E 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 198 " - pdb=" SG  CYS D 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 198 " - pdb=" SG  CYS G 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 198 " - pdb=" SG  CYS F 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 198 " - pdb=" SG  CYS I 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 198 " - pdb=" SG  CYS H 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 198 " - pdb=" SG  CYS K 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 198 " - pdb=" SG  CYS J 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 198 " - pdb=" SG  CYS L 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: 4.55
  Conformation dependent library (CDL) restraints added in 2.4 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: 1.94
  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: 5.31

  Time building geometry restraints manager: 5.26 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: 11006
       13.78 -    27.56: 994
       27.56 -    41.34: 217
       41.34 -    55.12: 95
       55.12 -    68.90: 24
  Dihedral angle restraints: 12336
    sinusoidal: 4728
      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 12333 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:
        2.32 -     2.84: 6476
        2.84 -     3.35: 18623
        3.35 -     3.87: 31246
        3.87 -     4.38: 38257
        4.38 -     4.90: 61702
  Nonbonded interactions: 156304
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 210 "
            pdb=" OE1 GLU C  71 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OE1 GLU A  71 "
            pdb=" OG1 THR B 210 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   SER H  44 "
            pdb=" OG  SER H  44 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   SER L  44 "
            pdb=" OG  SER L  44 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   SER I  44 "
            pdb=" OG  SER I  44 "
     model   vdw
     2.366 3.040
  ... (remaining 156299 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: 0.18
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:             2.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.750
  Check model and map are aligned:         0.130
  Set scattering table:                    0.160
  Process input model:                     34.620
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.610
-------------------------------------------------------------------------------
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   0.070  20112  Z= 0.203
  Angle     :  0.669   7.005  27372  Z= 0.438
  Chirality :  0.044   0.174   3168
  Planarity :  0.006   0.049   3552
  Dihedral  : 11.921  68.899   7320
  Min Nonbonded Distance : 2.319

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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30390 ( 1128)
  hydrogen bonds       : angle       8.92783 ( 3348)
  SS BOND              : bond        0.02210 (   24)
  SS BOND              : angle       1.11765 (   48)
  covalent geometry    : bond        0.00340 (20088)
  covalent geometry    : angle       0.66829 (27324)

*********************** 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  : 2.332 
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: 0.2946
  time to fit residues: 164.8919
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  : 1.996 
-------------------------------------------------------------------------------
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 112 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 112 GLN
G 193 ASN
H   4 GLN
H 193 ASN
I   4 GLN
I 112 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: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.184808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.130103 restraints weight = 20627.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.65
r_work: 0.3343 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  20112  Z= 0.182
  Angle     :  0.564   5.890  27372  Z= 0.294
  Chirality :  0.045   0.131   3168
  Planarity :  0.005   0.039   3552
  Dihedral  :  4.239  19.697   2784
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.29 %
    Favored  : 91.97 %
  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: -1.91 (0.14), residues: 2604
  helix: -0.99 (0.11), residues: 1644
  sheet:  None (None), residues: 0
  loop : -1.52 (0.18), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP F 117 
 HIS   0.003   0.001   HIS E  84 
 PHE   0.014   0.002   PHE A  32 
 TYR   0.015   0.002   TYR K 130 
 ARG   0.003   0.001   ARG H 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04645 ( 1128)
  hydrogen bonds       : angle       4.42039 ( 3348)
  SS BOND              : bond        0.00055 (   24)
  SS BOND              : angle       0.80437 (   48)
  covalent geometry    : bond        0.00442 (20088)
  covalent geometry    : angle       0.56345 (27324)

*********************** 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
  301 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 286
  time to evaluate  : 2.190 
Fit side-chains
REVERT: A   33 SER cc_start: 0.8970 (m) cc_final: 0.8673 (t)
REVERT: B   82 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7153 (ttp80)
REVERT: C   82 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7185 (ttp80)
REVERT: D   82 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7169 (ttp80)
REVERT: E   82 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7221 (ttp80)
REVERT: F   82 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7171 (ttp80)
REVERT: G   82 ARG cc_start: 0.7493 (ttp80) cc_final: 0.7135 (ttp80)
REVERT: J   82 ARG cc_start: 0.7465 (ttp80) cc_final: 0.7097 (ttp80)
REVERT: K   82 ARG cc_start: 0.7343 (ttp80) cc_final: 0.7142 (ttp80)
  outliers start: 15
  outliers final: 15
  residues processed: 292
  average time/residue: 0.3141
  time to fit residues: 138.4547
Evaluate side-chains
  300 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 285
  time to evaluate  : 1.964 
-------------------------------------------------------------------------------
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   11 VAL
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain D 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 K residue  136 LEU
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:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 133 optimal weight:    0.9990
   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:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   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 = 0.4157 r_free = 0.4157 target = 0.187033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.131812 restraints weight = 20499.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.67
r_work: 0.3349 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  20112  Z= 0.113
  Angle     :  0.464   5.271  27372  Z= 0.236
  Chirality :  0.042   0.134   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  4.007  18.835   2784
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.73 %
    Favored  : 89.72 %
  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: -0.67 (0.15), residues: 2604
  helix:  0.17 (0.12), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.44 (0.18), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  23 
 HIS   0.001   0.000   HIS I  84 
 PHE   0.011   0.002   PHE H  32 
 TYR   0.010   0.001   TYR D 169 
 ARG   0.005   0.000   ARG A 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 ( 1128)
  hydrogen bonds       : angle       4.01948 ( 3348)
  SS BOND              : bond        0.00100 (   24)
  SS BOND              : angle       0.42913 (   48)
  covalent geometry    : bond        0.00265 (20088)
  covalent geometry    : angle       0.46361 (27324)

*********************** 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
  302 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 291
  time to evaluate  : 2.007 
Fit side-chains
REVERT: C   82 ARG cc_start: 0.7385 (ttp80) cc_final: 0.7110 (ttp80)
REVERT: E   82 ARG cc_start: 0.7495 (ttp80) cc_final: 0.7208 (ttp80)
  outliers start: 11
  outliers final: 8
  residues processed: 297
  average time/residue: 0.3096
  time to fit residues: 139.4317
Evaluate side-chains
  279 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 271
  time to evaluate  : 2.035 
-------------------------------------------------------------------------------
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  102 SER
Chi-restraints excluded: chain C residue  144 MET
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue  102 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 222 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0770
   chunk 45 optimal weight:    1.9990
   chunk 251 optimal weight:    0.9990
   chunk 123 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 210 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 194 optimal weight:    0.9980
   chunk 179 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.6740

-------------------------------------------------------------------------------
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 = 0.4164 r_free = 0.4164 target = 0.187688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.133023 restraints weight = 20482.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.65
r_work: 0.3367 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  20112  Z= 0.101
  Angle     :  0.432   4.511  27372  Z= 0.219
  Chirality :  0.041   0.129   3168
  Planarity :  0.004   0.040   3552
  Dihedral  :  3.915  19.385   2784
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.38 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.03 (0.16), residues: 2604
  helix:  0.78 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.43 (0.18), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  23 
 HIS   0.001   0.000   HIS D  84 
 PHE   0.011   0.002   PHE H  32 
 TYR   0.010   0.001   TYR A 169 
 ARG   0.006   0.000   ARG A 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 ( 1128)
  hydrogen bonds       : angle       3.82878 ( 3348)
  SS BOND              : bond        0.00242 (   24)
  SS BOND              : angle       0.57962 (   48)
  covalent geometry    : bond        0.00239 (20088)
  covalent geometry    : angle       0.43146 (27324)

*********************** 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
  313 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 288
  time to evaluate  : 2.002 
Fit side-chains
REVERT: C   82 ARG cc_start: 0.7468 (ttp80) cc_final: 0.7133 (ttp80)
REVERT: C  103 ASP cc_start: 0.8455 (m-30) cc_final: 0.8205 (m-30)
REVERT: E  103 ASP cc_start: 0.8462 (m-30) cc_final: 0.8201 (m-30)
REVERT: I   82 ARG cc_start: 0.7452 (ttp80) cc_final: 0.7149 (ttp80)
REVERT: I  103 ASP cc_start: 0.8473 (m-30) cc_final: 0.8223 (m-30)
REVERT: L  103 ASP cc_start: 0.8466 (m-30) cc_final: 0.8216 (m-30)
  outliers start: 25
  outliers final: 19
  residues processed: 295
  average time/residue: 0.3135
  time to fit residues: 140.0797
Evaluate side-chains
  302 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 283
  time to evaluate  : 2.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
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  102 SER
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   11 VAL
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  102 SER
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  102 SER
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:    0.6980
   chunk 138 optimal weight:    0.0770
   chunk 211 optimal weight:    0.9980
   chunk 137 optimal weight:    0.7980
   chunk 113 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 158 optimal weight:    2.9990
   chunk 243 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.1140

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.186227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131092 restraints weight = 20660.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.65
r_work: 0.3329 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  20112  Z= 0.133
  Angle     :  0.450   4.458  27372  Z= 0.228
  Chirality :  0.043   0.134   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.968  19.215   2784
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.58 %
    Favored  : 88.27 %
  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:  0.19 (0.16), residues: 2604
  helix:  1.01 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.46 (0.18), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  23 
 HIS   0.002   0.001   HIS D  84 
 PHE   0.013   0.002   PHE A  32 
 TYR   0.009   0.001   TYR A 169 
 ARG   0.006   0.000   ARG A 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03467 ( 1128)
  hydrogen bonds       : angle       3.91269 ( 3348)
  SS BOND              : bond        0.00104 (   24)
  SS BOND              : angle       0.50508 (   48)
  covalent geometry    : bond        0.00325 (20088)
  covalent geometry    : angle       0.45013 (27324)

*********************** 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
  307 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 284
  time to evaluate  : 2.008 
Fit side-chains
REVERT: C   82 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7142 (ttp80)
  outliers start: 23
  outliers final: 21
  residues processed: 291
  average time/residue: 0.3087
  time to fit residues: 135.7289
Evaluate side-chains
  296 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 275
  time to evaluate  : 1.967 
-------------------------------------------------------------------------------
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 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  102 SER
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  102 SER
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  102 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0170
   chunk 213 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 239 optimal weight:    0.0670
   chunk 5 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.4956

-------------------------------------------------------------------------------
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 = 0.4163 r_free = 0.4163 target = 0.187906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.133319 restraints weight = 20378.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.65
r_work: 0.3372 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  20112  Z= 0.085
  Angle     :  0.405   4.305  27372  Z= 0.205
  Chirality :  0.040   0.128   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.794  19.594   2784
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.53 %
    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:  0.56 (0.16), residues: 2604
  helix:  1.34 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.39 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  23 
 HIS   0.001   0.000   HIS K  12 
 PHE   0.009   0.001   PHE L  32 
 TYR   0.009   0.001   TYR A 169 
 ARG   0.006   0.000   ARG A 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02827 ( 1128)
  hydrogen bonds       : angle       3.76603 ( 3348)
  SS BOND              : bond        0.00067 (   24)
  SS BOND              : angle       0.38550 (   48)
  covalent geometry    : bond        0.00199 (20088)
  covalent geometry    : angle       0.40535 (27324)

*********************** 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
  325 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 297
  time to evaluate  : 2.121 
Fit side-chains
REVERT: A   82 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7359 (ttp80)
REVERT: C   82 ARG cc_start: 0.7515 (ttp80) cc_final: 0.7187 (ttp80)
REVERT: C  103 ASP cc_start: 0.8467 (m-30) cc_final: 0.8216 (m-30)
REVERT: E  103 ASP cc_start: 0.8488 (m-30) cc_final: 0.8237 (m-30)
REVERT: I   82 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7212 (ttp80)
REVERT: I  103 ASP cc_start: 0.8477 (m-30) cc_final: 0.8208 (m-30)
REVERT: L  103 ASP cc_start: 0.8468 (m-30) cc_final: 0.8221 (m-30)
  outliers start: 28
  outliers final: 17
  residues processed: 301
  average time/residue: 0.3290
  time to fit residues: 147.7572
Evaluate side-chains
  300 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 283
  time to evaluate  : 2.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
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  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  102 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 192 optimal weight:    2.9990
   chunk 197 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 191 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 134 optimal weight:    0.4980
   chunk 182 optimal weight:    2.9990
   chunk 154 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 247 optimal weight:    0.8980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4141 r_free = 0.4141 target = 0.185595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.130503 restraints weight = 20425.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.65
r_work: 0.3335 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  20112  Z= 0.122
  Angle     :  0.437   4.462  27372  Z= 0.220
  Chirality :  0.042   0.132   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.874  19.423   2784
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.18 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.59 (0.16), residues: 2604
  helix:  1.35 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.36 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  23 
 HIS   0.002   0.001   HIS D  84 
 PHE   0.012   0.002   PHE H  32 
 TYR   0.008   0.001   TYR A 169 
 ARG   0.007   0.000   ARG F 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 ( 1128)
  hydrogen bonds       : angle       3.84359 ( 3348)
  SS BOND              : bond        0.00067 (   24)
  SS BOND              : angle       0.33957 (   48)
  covalent geometry    : bond        0.00299 (20088)
  covalent geometry    : angle       0.43675 (27324)

*********************** 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
  301 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 275
  time to evaluate  : 1.898 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8490 (m-30) cc_final: 0.8240 (m-30)
REVERT: E  103 ASP cc_start: 0.8512 (m-30) cc_final: 0.8255 (m-30)
REVERT: I   82 ARG cc_start: 0.7449 (ttp80) cc_final: 0.7123 (ttp80)
REVERT: L  103 ASP cc_start: 0.8492 (m-30) cc_final: 0.8239 (m-30)
  outliers start: 26
  outliers final: 22
  residues processed: 283
  average time/residue: 0.3450
  time to fit residues: 144.2735
Evaluate side-chains
  296 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 274
  time to evaluate  : 2.202 
-------------------------------------------------------------------------------
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 A residue  210 THR
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  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   66 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  102 SER
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  102 SER
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:    0.6980
   chunk 211 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 110 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9980
   chunk 157 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 116 optimal weight:    0.9980
   chunk 225 optimal weight:    6.9990
   chunk 216 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4149 r_free = 0.4149 target = 0.186369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.131421 restraints weight = 20455.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.66
r_work: 0.3346 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  20112  Z= 0.102
  Angle     :  0.420   4.417  27372  Z= 0.212
  Chirality :  0.041   0.130   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.800  19.589   2784
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.28 %
    Favored  : 87.33 %
  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:  0.73 (0.17), residues: 2604
  helix:  1.47 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.33 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  23 
 HIS   0.001   0.000   HIS E  84 
 PHE   0.010   0.001   PHE H  32 
 TYR   0.009   0.001   TYR A 169 
 ARG   0.006   0.000   ARG A 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02991 ( 1128)
  hydrogen bonds       : angle       3.79702 ( 3348)
  SS BOND              : bond        0.00069 (   24)
  SS BOND              : angle       0.37921 (   48)
  covalent geometry    : bond        0.00247 (20088)
  covalent geometry    : angle       0.42044 (27324)

*********************** 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
  312 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 284
  time to evaluate  : 2.004 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8475 (m-30) cc_final: 0.8237 (m-30)
REVERT: E  103 ASP cc_start: 0.8518 (m-30) cc_final: 0.8259 (m-30)
REVERT: E  154 ARG cc_start: 0.7578 (mtt-85) cc_final: 0.7375 (mtt-85)
REVERT: I   82 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7144 (ttp80)
REVERT: I  103 ASP cc_start: 0.8510 (m-30) cc_final: 0.8226 (m-30)
REVERT: I  154 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7289 (mtt-85)
REVERT: L  103 ASP cc_start: 0.8489 (m-30) cc_final: 0.8244 (m-30)
REVERT: L  154 ARG cc_start: 0.7567 (mtt-85) cc_final: 0.7282 (mtt-85)
  outliers start: 28
  outliers final: 24
  residues processed: 289
  average time/residue: 0.3475
  time to fit residues: 147.7428
Evaluate side-chains
  305 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 281
  time to evaluate  : 2.001 
-------------------------------------------------------------------------------
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 A residue  210 THR
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue  102 SER
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  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   66 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  102 SER
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  102 SER
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:    0.0270
   chunk 88 optimal weight:    0.5980
   chunk 197 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 105 optimal weight:    0.4980
   chunk 216 optimal weight:    4.9990
   chunk 215 optimal weight:    0.0370
   chunk 220 optimal weight:    2.9990
   chunk 166 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 133 optimal weight:    0.7980
   overall best weight:    0.3916

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.189535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.134937 restraints weight = 20451.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.65
r_work: 0.3385 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  20112  Z= 0.081
  Angle     :  0.406   4.328  27372  Z= 0.204
  Chirality :  0.040   0.127   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.698  19.778   2784
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.48 %
    Favored  : 87.28 %
  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:  0.89 (0.17), residues: 2604
  helix:  1.63 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.33 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  23 
 HIS   0.003   0.000   HIS C  84 
 PHE   0.009   0.001   PHE H  32 
 TYR   0.009   0.001   TYR C 169 
 ARG   0.008   0.000   ARG F 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02671 ( 1128)
  hydrogen bonds       : angle       3.70702 ( 3348)
  SS BOND              : bond        0.00072 (   24)
  SS BOND              : angle       0.40125 (   48)
  covalent geometry    : bond        0.00188 (20088)
  covalent geometry    : angle       0.40622 (27324)

*********************** 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
  324 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 299
  time to evaluate  : 2.014 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8482 (m-30) cc_final: 0.8245 (m-30)
REVERT: C  154 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7282 (mtt-85)
REVERT: D  121 ASN cc_start: 0.8018 (t0) cc_final: 0.6976 (m-40)
REVERT: E  103 ASP cc_start: 0.8502 (m-30) cc_final: 0.8256 (m-30)
REVERT: I   82 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7291 (ttp80)
REVERT: I  103 ASP cc_start: 0.8506 (m-30) cc_final: 0.8239 (m-30)
REVERT: J   25 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8126 (mmmt)
REVERT: J  121 ASN cc_start: 0.8015 (t0) cc_final: 0.7080 (m-40)
REVERT: L  103 ASP cc_start: 0.8522 (m-30) cc_final: 0.8295 (m-30)
REVERT: L  154 ARG cc_start: 0.7542 (mtt-85) cc_final: 0.7230 (mtt-85)
  outliers start: 25
  outliers final: 20
  residues processed: 306
  average time/residue: 0.3386
  time to fit residues: 153.4118
Evaluate side-chains
  318 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 298
  time to evaluate  : 2.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
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  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  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain H residue   66 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  102 SER
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  144 MET
Chi-restraints excluded: chain L residue  102 SER
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:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 116 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 200 optimal weight:    4.9990
   chunk 155 optimal weight:    0.0470
   chunk 126 optimal weight:    0.0570
   chunk 86 optimal weight:    0.8980
   chunk 206 optimal weight:    3.9990
   overall best weight:    0.9998

-------------------------------------------------------------------------------
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 = 0.4141 r_free = 0.4141 target = 0.185321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.130216 restraints weight = 20372.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.67
r_work: 0.3332 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  20112  Z= 0.123
  Angle     :  0.444   4.510  27372  Z= 0.223
  Chirality :  0.042   0.131   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.824  19.453   2784
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.73 %
    Favored  : 87.28 %
  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:  0.82 (0.17), residues: 2604
  helix:  1.56 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.32 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  23 
 HIS   0.002   0.001   HIS E  84 
 PHE   0.012   0.002   PHE H  32 
 TYR   0.008   0.001   TYR A 169 
 ARG   0.009   0.001   ARG E 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03139 ( 1128)
  hydrogen bonds       : angle       3.80146 ( 3348)
  SS BOND              : bond        0.00082 (   24)
  SS BOND              : angle       0.56245 (   48)
  covalent geometry    : bond        0.00304 (20088)
  covalent geometry    : angle       0.44373 (27324)

********************** 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
  308 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 288
  time to evaluate  : 2.205 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8501 (m-30) cc_final: 0.8263 (m-30)
REVERT: E  103 ASP cc_start: 0.8512 (m-30) cc_final: 0.8266 (m-30)
REVERT: I  103 ASP cc_start: 0.8524 (m-30) cc_final: 0.8265 (m-30)
REVERT: J   25 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8100 (mmmt)
REVERT: L  103 ASP cc_start: 0.8490 (m-30) cc_final: 0.8257 (m-30)
  outliers start: 20
  outliers final: 19
  residues processed: 292
  average time/residue: 0.3475
  time to fit residues: 149.8639
Evaluate side-chains
  305 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 286
  time to evaluate  : 2.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
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   11 VAL
Chi-restraints excluded: chain H residue   66 MET
Chi-restraints excluded: chain H residue  144 MET
Chi-restraints excluded: chain I residue  102 SER
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  144 MET
Chi-restraints excluded: chain L residue  102 SER
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:    0.0980
   chunk 49 optimal weight:    0.6980
   chunk 189 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   chunk 190 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 180 optimal weight:    0.5980
   chunk 103 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 111 optimal weight:    0.6980
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.187155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.132338 restraints weight = 20490.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.65
r_work: 0.3358 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  20112  Z= 0.090
  Angle     :  0.421   4.406  27372  Z= 0.211
  Chirality :  0.041   0.129   3168
  Planarity :  0.004   0.038   3552
  Dihedral  :  3.752  19.678   2784
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  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:  0.95 (0.17), residues: 2604
  helix:  1.69 (0.13), residues: 1656
  sheet:  None (None), residues: 0
  loop : -1.33 (0.19), residues: 948

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02805 ( 1128)
  hydrogen bonds       : angle       3.75695 ( 3348)
  SS BOND              : bond        0.00091 (   24)
  SS BOND              : angle       0.52831 (   48)
  covalent geometry    : bond        0.00214 (20088)
  covalent geometry    : angle       0.42074 (27324)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8654.45 seconds
wall clock time: 150 minutes 52.42 seconds (9052.42 seconds total)