Starting phenix.real_space_refine
on Wed Feb 12 08:36:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uan_20708/02_2025/6uan_20708.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uan_20708/02_2025/6uan_20708.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uan_20708/02_2025/6uan_20708.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uan_20708/02_2025/6uan_20708.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uan_20708/02_2025/6uan_20708.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uan_20708/02_2025/6uan_20708.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      32      5.16       5
     C    4884      2.51       5
     N    1318      2.21       5
     O    1449      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7685
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1847
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "Z"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1746
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 224}
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 70
    Chain: "B"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2022
          Classifications: {'peptide': 261}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 13, 'TRANS': 247}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 37
    Chain: "C"
      Number of atoms: 2070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2070
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 13, 'TRANS': 271}
          Unresolved non-hydrogen bonds: 219
          Unresolved non-hydrogen angles: 265
          Unresolved non-hydrogen dihedrals: 189
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 132
  Time building chain proxies: 4.58, per 1000 atoms: 0.60
  Number of scatterers: 7685
  At special positions: 0
  Unit cell: (94.34, 98.58, 106, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P       2     15.00
     O    1449      8.00
     N    1318      7.00
     C    4884      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      55.9% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 13
      removed outlier: 3.616A  pdb=" N   GLU A   6 " --> pdb=" O   VAL A   2 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A   7 " --> pdb=" O   ASP A   3 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG A  10 " --> pdb=" O   GLU A   6 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA A  11 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 28
      removed outlier: 4.631A  pdb=" N   ALA A  26 " --> pdb=" O   ASP A  22 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 31
      No H-bonds generated for 'chain 'A' and resid 29 through 31'
    Processing helix  chain 'A' and resid 38 through 68
      removed outlier: 3.764A  pdb=" N   ASN A  43 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   LEU A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU A  45 " --> pdb=" O   GLU A  41 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL A  53 " --> pdb=" O   TYR A  49 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ARG A  56 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER A  58 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL A  62 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 105
      removed outlier: 3.837A  pdb=" N   ALA A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LYS A  86 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A  87 " --> pdb=" O   TYR A  83 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   GLU A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   CYS A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   TYR A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   ASP A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   VAL A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   HIS A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 110
      removed outlier: 3.513A  pdb=" N   LYS A 109 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 129
      removed outlier: 3.601A  pdb=" N   TYR A 126 " --> pdb=" O   MET A 122 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   TYR A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ARG A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 159
      removed outlier: 4.062A  pdb=" N   VAL A 143 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   GLU A 144 " --> pdb=" O   ASN A 140 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ASP A 145 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLU A 155 " --> pdb=" O   GLN A 151 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ILE A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 182
      removed outlier: 3.893A  pdb=" N   VAL A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 178 " --> pdb=" O   ASN A 174 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   TYR A 179 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   TYR A 180 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLU A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 202
      removed outlier: 4.381A  pdb=" N   GLN A 195 " --> pdb=" O   GLN A 191 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ALA A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 231
      removed outlier: 3.579A  pdb=" N   ASP A 214 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU A 221 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU A 228 " --> pdb=" O   ASP A 224 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TRP A 229 " --> pdb=" O   ASN A 225 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 4 through 18
      removed outlier: 3.859A  pdb=" N   ALA Z  11 " --> pdb=" O   LEU Z   7 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN Z  16 " --> pdb=" O   LYS Z  12 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA Z  17 " --> pdb=" O   LEU Z  13 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 19 through 31
      removed outlier: 3.548A  pdb=" N   MET Z  23 " --> pdb=" O   ARG Z  19 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   MET Z  27 " --> pdb=" O   MET Z  23 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS Z  28 " --> pdb=" O   ALA Z  24 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU Z  29 " --> pdb=" O   ALA Z  25 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL Z  30 " --> pdb=" O   ALA Z  26 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR Z  31 " --> pdb=" O   MET Z  27 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 41 through 69
      removed outlier: 3.868A  pdb=" N   LEU Z  45 " --> pdb=" O   GLU Z  41 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   SER Z  46 " --> pdb=" O   ARG Z  42 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL Z  47 " --> pdb=" O   ASN Z  43 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG Z  56 " --> pdb=" O   VAL Z  52 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER Z  59 " --> pdb=" O   ALA Z  55 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   VAL Z  62 " --> pdb=" O   SER Z  58 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER Z  65 " --> pdb=" O   ARG Z  61 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLN Z  68 " --> pdb=" O   SER Z  64 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 73 through 105
      removed outlier: 3.718A  pdb=" N   TYR Z  83 " --> pdb=" O   MET Z  79 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL Z  85 " --> pdb=" O   LYS Z  81 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS Z  86 " --> pdb=" O   GLU Z  82 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL Z  87 " --> pdb=" O   TYR Z  83 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU Z  88 " --> pdb=" O   ARG Z  84 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLU Z  93 " --> pdb=" O   LYS Z  89 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE Z  94 " --> pdb=" O   GLU Z  90 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   CYS Z  95 " --> pdb=" O   LEU Z  91 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ASP Z  97 " --> pdb=" O   GLU Z  93 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS Z 104 " --> pdb=" O   GLY Z 100 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 105 through 110
    Processing helix  chain 'Z' and resid 115 through 134
      removed outlier: 3.688A  pdb=" N   TYR Z 119 " --> pdb=" O   SER Z 115 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU Z 120 " --> pdb=" O   LYS Z 116 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY Z 124 " --> pdb=" O   LEU Z 120 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TYR Z 126 " --> pdb=" O   MET Z 122 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR Z 127 " --> pdb=" O   LYS Z 123 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL Z 133 " --> pdb=" O   TYR Z 129 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 136 through 155
      removed outlier: 3.987A  pdb=" N   ASN Z 140 " --> pdb=" O   GLY Z 136 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL Z 142 " --> pdb=" O   THR Z 138 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU Z 144 " --> pdb=" O   ASN Z 140 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ASP Z 145 " --> pdb=" O   SER Z 141 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS Z 148 " --> pdb=" O   GLU Z 144 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASP Z 152 " --> pdb=" O   LYS Z 148 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ALA Z 153 " --> pdb=" O   ALA Z 149 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 165 through 182
      removed outlier: 3.549A  pdb=" N   ALA Z 172 " --> pdb=" O   ARG Z 168 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   TYR Z 179 " --> pdb=" O   PHE Z 175 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR Z 180 " --> pdb=" O   SER Z 176 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 188 through 202
      removed outlier: 3.706A  pdb=" N   LEU Z 192 " --> pdb=" O   LYS Z 188 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA Z 193 " --> pdb=" O   ALA Z 189 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASP Z 199 " --> pdb=" O   GLN Z 195 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA Z 202 " --> pdb=" O   ASP Z 198 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 212 through 231
      removed outlier: 3.834A  pdb=" N   LEU Z 217 " --> pdb=" O   LYS Z 213 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ILE Z 218 " --> pdb=" O   ASP Z 214 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG Z 223 " --> pdb=" O   MET Z 219 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   THR Z 227 " --> pdb=" O   ARG Z 223 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   LEU Z 228 " --> pdb=" O   ASP Z 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 506
      removed outlier: 4.473A  pdb=" N   LYS B 499 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASN B 500 " --> pdb=" O   GLN B 496 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLY B 503 " --> pdb=" O   LYS B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 542
    Processing helix  chain 'B' and resid 549 through 554
      removed outlier: 3.702A  pdb=" N   ILE B 554 " --> pdb=" O   MET B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 570
      removed outlier: 3.987A  pdb=" N   GLN B 559 " --> pdb=" O   ASP B 555 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA B 561 " --> pdb=" O   ALA B 557 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLY B 563 " --> pdb=" O   GLN B 559 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ASP B 565 " --> pdb=" O   ALA B 561 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TYR B 566 " --> pdb=" O   GLN B 562 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU B 567 " --> pdb=" O   GLY B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 580
      No H-bonds generated for 'chain 'B' and resid 578 through 580'
    Processing helix  chain 'B' and resid 584 through 588
      removed outlier: 3.586A  pdb=" N   ASP B 587 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 637
      removed outlier: 3.537A  pdb=" N   SER B 637 " --> pdb=" O   SER B 634 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 634 through 637'
    Processing helix  chain 'B' and resid 638 through 652
      removed outlier: 4.319A  pdb=" N   ILE B 644 " --> pdb=" O   TYR B 640 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   MET B 650 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 695
    Processing helix  chain 'B' and resid 700 through 704
      removed outlier: 3.953A  pdb=" N   ARG B 704 " --> pdb=" O   ARG B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 707 through 719
      removed outlier: 3.502A  pdb=" N   ALA B 712 " --> pdb=" O   PRO B 708 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER B 713 " --> pdb=" O   GLN B 709 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 714 " --> pdb=" O   ILE B 710 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   LEU B 717 " --> pdb=" O   SER B 713 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ARG B 719 " --> pdb=" O   GLU B 715 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 491 through 505
      removed outlier: 3.634A  pdb=" N   GLN C 496 " --> pdb=" O   PRO C 492 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   GLY C 503 " --> pdb=" O   LYS C 499 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 537 through 543
    Processing helix  chain 'C' and resid 553 through 560
      removed outlier: 3.505A  pdb=" N   ALA C 557 " --> pdb=" O   LEU C 553 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN C 559 " --> pdb=" O   ASP C 555 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 564 through 570
    Processing helix  chain 'C' and resid 621 through 627
    Processing helix  chain 'C' and resid 638 through 651
    Processing helix  chain 'C' and resid 664 through 669
      removed outlier: 3.864A  pdb=" N   MET C 668 " --> pdb=" O   GLN C 664 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 686 through 697
      removed outlier: 4.205A  pdb=" N   MET C 693 " --> pdb=" O   MET C 689 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA C 694 " --> pdb=" O   LYS C 690 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU C 695 " --> pdb=" O   ARG C 691 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LEU C 697 " --> pdb=" O   MET C 693 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 706 through 715
      removed outlier: 4.012A  pdb=" N   ILE C 714 " --> pdb=" O   ILE C 710 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 462 through 466
      removed outlier: 3.851A  pdb=" N   VAL B 471 " --> pdb=" O   ILE B 463 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   SER B 465 " --> pdb=" O   GLY B 469 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   GLY B 469 " --> pdb=" O   SER B 465 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 582 through 583
    Processing sheet with id=AA3, first strand: chain 'C' and resid 462 through 465
      removed outlier: 6.402A  pdb=" N   ARG C 462 " --> pdb=" O   LYS C 473 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   LYS C 473 " --> pdb=" O   ARG C 462 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY C 464 " --> pdb=" O   VAL C 471 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   THR C 470 " --> pdb=" O   MET C 484 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL C 482 " --> pdb=" O   TYR C 472 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ALA C 481 " --> pdb=" O   THR C 529 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR C 529 " --> pdb=" O   ALA C 481 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 534 through 536
      removed outlier: 3.880A  pdb=" N   SER C 535 " --> pdb=" O   LEU C 584 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR C 589 " --> pdb=" O   HIS C 585 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 572 through 573

    304 hydrogen bonds defined for protein.
    885 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2244
        1.33 -     1.45: 1202
        1.45 -     1.57: 4321
        1.57 -     1.69: 8
        1.69 -     1.81: 53
  Bond restraints: 7828
  Sorted by residual:
  bond pdb=" N   SER C 720 "
       pdb=" CA  SER C 720 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 5.01e+00
  bond pdb=" C   ILE A 107 "
       pdb=" N   PRO A 108 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.17e+00
  bond pdb=" C   LYS C 522 "
       pdb=" N   PRO C 523 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.59e+00
  bond pdb=" C   LYS B 522 "
       pdb=" N   PRO B 523 "
    ideal  model  delta    sigma   weight residual
    1.334  1.377 -0.043 2.34e-02 1.83e+03 3.43e+00
  bond pdb=" CA  SEP B 729 "
       pdb=" C   SEP B 729 "
    ideal  model  delta    sigma   weight residual
    1.525  1.488  0.037 2.10e-02 2.27e+03 3.14e+00
  ... (remaining 7823 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 10170
        2.05 -     4.10: 381
        4.10 -     6.14: 40
        6.14 -     8.19: 17
        8.19 -    10.24: 8
  Bond angle restraints: 10616
  Sorted by residual:
  angle pdb=" C   HIS B 574 "
        pdb=" N   ARG B 575 "
        pdb=" CA  ARG B 575 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" C   HIS C 585 "
        pdb=" N   GLU C 586 "
        pdb=" CA  GLU C 586 "
      ideal   model   delta    sigma   weight residual
     121.54  128.31   -6.77 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" CG1 ILE C 582 "
        pdb=" CB  ILE C 582 "
        pdb=" CG2 ILE C 582 "
      ideal   model   delta    sigma   weight residual
     110.70  101.20    9.50 3.00e+00 1.11e-01 1.00e+01
  angle pdb=" CA  LEU B 525 "
        pdb=" CB  LEU B 525 "
        pdb=" CG  LEU B 525 "
      ideal   model   delta    sigma   weight residual
     116.30  126.54  -10.24 3.50e+00 8.16e-02 8.56e+00
  angle pdb=" CA  ILE A 107 "
        pdb=" C   ILE A 107 "
        pdb=" N   PRO A 108 "
      ideal   model   delta    sigma   weight residual
     120.83  122.60   -1.77 6.10e-01 2.69e+00 8.45e+00
  ... (remaining 10611 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 4140
       17.14 -    34.28: 462
       34.28 -    51.41: 111
       51.41 -    68.55: 16
       68.55 -    85.69: 14
  Dihedral angle restraints: 4743
    sinusoidal: 1786
      harmonic: 2957
  Sorted by residual:
  dihedral pdb=" CA  LYS A 158 "
           pdb=" C   LYS A 158 "
           pdb=" N   ALA A 159 "
           pdb=" CA  ALA A 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.16   23.84     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  VAL Z  35 "
           pdb=" C   VAL Z  35 "
           pdb=" N   GLU Z  36 "
           pdb=" CA  GLU Z  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.67  -22.33     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  ASP B 555 "
           pdb=" C   ASP B 555 "
           pdb=" N   ILE B 556 "
           pdb=" CA  ILE B 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.86   22.14     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 4740 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 857
       0.054 -    0.109: 299
       0.109 -    0.163: 51
       0.163 -    0.218: 10
       0.218 -    0.272: 1
  Chirality restraints: 1218
  Sorted by residual:
  chirality pdb=" CB  VAL C 590 "
            pdb=" CA  VAL C 590 "
            pdb=" CG1 VAL C 590 "
            pdb=" CG2 VAL C 590 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CB  ILE B 724 "
            pdb=" CA  ILE B 724 "
            pdb=" CG1 ILE B 724 "
            pdb=" CG2 ILE B 724 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  ILE C 457 "
            pdb=" CA  ILE C 457 "
            pdb=" CG1 ILE C 457 "
            pdb=" CG2 ILE C 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1215 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 491 "    0.050 5.00e-02 4.00e+02   7.62e-02 9.28e+00
        pdb=" N   PRO C 492 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO C 492 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C 492 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 707 "   -0.039 5.00e-02 4.00e+02   5.86e-02 5.50e+00
        pdb=" N   PRO C 708 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO C 708 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 708 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 721 "    0.033 5.00e-02 4.00e+02   4.95e-02 3.93e+00
        pdb=" N   PRO C 722 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C 722 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 722 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 2021
        2.78 -     3.31: 7213
        3.31 -     3.84: 12231
        3.84 -     4.37: 13985
        4.37 -     4.90: 22973
  Nonbonded interactions: 58423
  Sorted by model distance:
  nonbonded pdb=" O   PHE Z 154 "
            pdb=" OG  SER Z 157 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG1 THR C 651 "
            pdb=" O   LYS C 680 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OG  SER Z  38 "
            pdb=" OE1 GLU Z  41 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ALA A 172 "
            pdb=" OG  SER A 176 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   ASN A 112 "
            pdb=" OG  SER A 115 "
     model   vdw
     2.293 3.040
  ... (remaining 58418 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 6 through 14 or (resid 15 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 16 through 17 or (resid 18 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 19 through 39 or (resid \ 
 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 
 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) or res \ 
id 70 through 73 or (resid 74 through 76 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 77 or (resid 78 through 80 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 81 through 92 or (resid 93 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 94 through 103 or (resid 10 \ 
4 and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ 
 or resid 105 through 113 or (resid 114 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 115 or (resid 116 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 117 through 121 or (resid 122 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 123 through 143 or (resid 144 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 145 through 160 or \ 
 (resid 161 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 
2 through 180 or (resid 181 and (name N or name CA or name C or name O or name C \ 
B )) or resid 182 through 194 or (resid 195 through 196 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 197 through 202 or (resid 203 through  \ 
206 and (name N or name CA or name C or name O or name CB )) or resid 207 throug \ 
h 208 or (resid 209 through 211 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 212 or (resid 213 through 214 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 215 through 219 or (resid 220 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 221 through 232))
  selection = (chain 'Z' and (resid 3 through 70 or (resid 71 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 72 through 232))
}
ncs_group {
  reference = (chain 'B' and (resid 449 through 485 or (resid 486 through 487 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 488 through 521 or (resid 522  \ 
and (name N or name CA or name C or name O or name CB )) or resid 523 through 54 \ 
6 or (resid 547 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 548 through 625 or (resid 626 through 631 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 632 through 647 or (resid 648 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 649 through 677 or (resid 678 thro \ 
ugh 685 and (name N or name CA or name C or name O or name CB )) or resid 686 or \ 
 (resid 687 through 691 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 692 or (resid 693 through 695 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 696 through 698 or (resid 699 through 703 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 704 through 718 or (resid  \ 
719 and (name N or name CA or name C or name O or name CB )) or resid 720 throug \ 
h 723 or (resid 724 through 725 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 726 through 729 or (resid 730 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 731 through 733))
  selection = (chain 'C' and (resid 449 through 600 or resid 622 through 628 or resid 631 thro \ 
ugh 649 or (resid 650 and (name N or name CA or name C or name O or name CB or n \ 
ame CG or name SD )) or resid 651 through 657 or resid 676 through 682 or (resid \ 
 683 through 685 and (name N or name CA or name C or name O or name CB )) or res \ 
id 686 through 733))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.660
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
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      :  0.007   0.055   7828  Z= 0.467
  Angle     :  0.946  10.241  10616  Z= 0.503
  Chirality :  0.056   0.272   1218
  Planarity :  0.006   0.076   1358
  Dihedral  : 16.091  85.692   2827
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.18 %
    Favored  : 84.79 %
  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: -5.36 (0.19), residues: 987
  helix: -4.03 (0.12), residues: 495
  sheet: -3.95 (0.58), residues: 42
  loop : -2.81 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 229 
 HIS   0.006   0.002   HIS C 585 
 PHE   0.023   0.003   PHE B 595 
 TYR   0.033   0.003   TYR A  49 
 ARG   0.008   0.001   ARG A 128 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 208
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Z    9 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7907 (tp-100)
REVERT: Z  150 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7760 (m-80)
REVERT: B  472 TYR cc_start: 0.7201 (m-10) cc_final: 0.6985 (m-80)
REVERT: B  484 MET cc_start: 0.7983 (ptp) cc_final: 0.7779 (ptp)
REVERT: B  506 ARG cc_start: 0.7864 (ttt90) cc_final: 0.7646 (mtt-85)
REVERT: B  548 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6452 (m-80)
REVERT: B  565 ASP cc_start: 0.8255 (t70) cc_final: 0.7999 (t0)
REVERT: B  581 ASN cc_start: 0.8311 (p0) cc_final: 0.8107 (p0)
REVERT: B  691 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8507 (ttm-80)
REVERT: B  703 GLU cc_start: 0.8800 (pp20) cc_final: 0.8316 (pp20)
REVERT: C  575 ARG cc_start: 0.8255 (ttt180) cc_final: 0.8017 (ttt-90)
REVERT: C  638 ASP cc_start: 0.9298 (t0) cc_final: 0.9002 (t0)
REVERT: C  697 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8632 (pp)
  outliers start: 8
  outliers final: 1
  residues processed: 215
  average time/residue: 0.2294
  time to fit residues: 63.8691
Evaluate side-chains
  157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 153
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue  150 TYR
Chi-restraints excluded: chain B residue  548 PHE
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  697 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 47 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 140 ASN
A 151 GLN
A 165 HIS
A 225 ASN
Z   9 GLN
Z 140 ASN
B 510 HIS
C 510 HIS
C 530 GLN
C 542 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.114532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.092932 restraints weight = 18052.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.095469 restraints weight = 11286.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.097198 restraints weight = 8313.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7828  Z= 0.178
  Angle     :  0.660  10.077  10616  Z= 0.347
  Chirality :  0.043   0.144   1218
  Planarity :  0.004   0.039   1358
  Dihedral  :  6.419  56.208   1096
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.91 %
    Favored  : 78.61 %
  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: -4.18 (0.21), residues: 987
  helix: -2.66 (0.16), residues: 537
  sheet: -3.31 (0.66), residues: 42
  loop : -2.69 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  60 
 HIS   0.006   0.001   HIS C 585 
 PHE   0.040   0.002   PHE A 154 
 TYR   0.032   0.002   TYR B 647 
 ARG   0.006   0.001   ARG B 575 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 200
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Z    9 GLN cc_start: 0.8557 (tp40) cc_final: 0.8276 (tp-100)
REVERT: Z  150 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7582 (m-80)
REVERT: B  484 MET cc_start: 0.8348 (ptp) cc_final: 0.8038 (ptt)
REVERT: B  548 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6857 (m-80)
REVERT: B  581 ASN cc_start: 0.8431 (p0) cc_final: 0.8178 (p0)
REVERT: B  703 GLU cc_start: 0.8867 (pp20) cc_final: 0.8155 (pp20)
REVERT: B  733 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5840 (tt)
REVERT: C  462 ARG cc_start: 0.7782 (tmm-80) cc_final: 0.7459 (ttt-90)
REVERT: C  545 GLU cc_start: 0.7737 (mp0) cc_final: 0.7473 (mp0)
REVERT: C  552 LYS cc_start: 0.8442 (pttt) cc_final: 0.7730 (pttm)
REVERT: C  577 LEU cc_start: 0.9310 (tp) cc_final: 0.9073 (tt)
REVERT: C  697 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8625 (pp)
  outliers start: 27
  outliers final: 9
  residues processed: 214
  average time/residue: 0.1791
  time to fit residues: 52.9579
Evaluate side-chains
  176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain Z residue    8 VAL
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  150 TYR
Chi-restraints excluded: chain Z residue  164 THR
Chi-restraints excluded: chain B residue  548 PHE
Chi-restraints excluded: chain B residue  695 GLU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain C residue  491 THR
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  697 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0060
   chunk 27 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 92 optimal weight:    8.9990
   chunk 49 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
Z 151 GLN
C 562 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.114902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.093249 restraints weight = 18278.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.095763 restraints weight = 11449.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.097516 restraints weight = 8454.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7828  Z= 0.169
  Angle     :  0.621   9.456  10616  Z= 0.317
  Chirality :  0.042   0.141   1218
  Planarity :  0.003   0.034   1358
  Dihedral  :  5.907  56.792   1096
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.01 %
    Favored  : 75.52 %
  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: -3.07 (0.23), residues: 987
  helix: -1.63 (0.19), residues: 535
  sheet: -2.79 (0.74), residues: 42
  loop : -2.38 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 531 
 HIS   0.007   0.001   HIS C 585 
 PHE   0.023   0.002   PHE Z 118 
 TYR   0.014   0.001   TYR A 180 
 ARG   0.005   0.000   ARG B 575 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 LYS cc_start: 0.8573 (mttt) cc_final: 0.8161 (mttm)
REVERT: A  154 PHE cc_start: 0.7116 (m-80) cc_final: 0.6646 (m-80)
REVERT: Z    9 GLN cc_start: 0.8514 (tp40) cc_final: 0.8290 (tp-100)
REVERT: B  517 MET cc_start: 0.7807 (mmm) cc_final: 0.7199 (mmt)
REVERT: B  548 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6768 (m-80)
REVERT: B  647 TYR cc_start: 0.8540 (t80) cc_final: 0.8147 (t80)
REVERT: B  711 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8009 (tp)
REVERT: B  733 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5718 (tt)
REVERT: C  462 ARG cc_start: 0.7914 (tmm-80) cc_final: 0.7560 (ttt-90)
REVERT: C  501 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8185 (mm-30)
REVERT: C  506 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8072 (ttm110)
REVERT: C  545 GLU cc_start: 0.7811 (mp0) cc_final: 0.7527 (mp0)
REVERT: C  552 LYS cc_start: 0.8436 (pttt) cc_final: 0.7625 (pttm)
REVERT: C  583 PHE cc_start: 0.7890 (t80) cc_final: 0.7626 (m-80)
REVERT: C  697 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8656 (pp)
  outliers start: 27
  outliers final: 15
  residues processed: 215
  average time/residue: 0.1759
  time to fit residues: 52.4154
Evaluate side-chains
  199 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain Z residue    8 VAL
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  138 THR
Chi-restraints excluded: chain Z residue  164 THR
Chi-restraints excluded: chain Z residue  175 PHE
Chi-restraints excluded: chain B residue  548 PHE
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  707 PHE
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  529 THR
Chi-restraints excluded: chain C residue  582 ILE
Chi-restraints excluded: chain C residue  592 ILE
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  677 ASP
Chi-restraints excluded: chain C residue  697 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0670
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    1.1922

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

Flipped N/Q/H residues before XYZ refinement:
B 542 HIS
B 581 ASN
B 709 GLN
C 540 HIS
C 562 GLN
C 581 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.114101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.093205 restraints weight = 18146.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.095667 restraints weight = 11284.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.097361 restraints weight = 8281.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7828  Z= 0.177
  Angle     :  0.616   8.719  10616  Z= 0.315
  Chirality :  0.042   0.140   1218
  Planarity :  0.003   0.032   1358
  Dihedral  :  5.634  57.173   1094
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 23.97 %
    Favored  : 71.65 %
  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: -2.49 (0.25), residues: 987
  helix: -1.11 (0.21), residues: 532
  sheet: -2.66 (0.76), residues: 42
  loop : -2.17 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 229 
 HIS   0.005   0.001   HIS C 585 
 PHE   0.039   0.002   PHE Z 197 
 TYR   0.017   0.001   TYR A 180 
 ARG   0.006   0.000   ARG Z  57 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 192
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8464 (mmtm)
REVERT: A  154 PHE cc_start: 0.7243 (m-80) cc_final: 0.6924 (m-80)
REVERT: Z    9 GLN cc_start: 0.8506 (tp40) cc_final: 0.8305 (tp-100)
REVERT: Z  212 TYR cc_start: 0.7884 (p90) cc_final: 0.7497 (p90)
REVERT: B  472 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7112 (m-10)
REVERT: B  517 MET cc_start: 0.7856 (mmm) cc_final: 0.7212 (mmt)
REVERT: B  548 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6746 (m-80)
REVERT: B  647 TYR cc_start: 0.8584 (t80) cc_final: 0.8378 (t80)
REVERT: B  648 GLU cc_start: 0.8366 (tp30) cc_final: 0.8111 (tp30)
REVERT: B  696 CYS cc_start: 0.8980 (m) cc_final: 0.8680 (m)
REVERT: B  733 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5868 (tt)
REVERT: C  462 ARG cc_start: 0.7921 (tmm-80) cc_final: 0.7588 (ttt-90)
REVERT: C  501 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8188 (mm-30)
REVERT: C  545 GLU cc_start: 0.7790 (mp0) cc_final: 0.7481 (mp0)
REVERT: C  552 LYS cc_start: 0.8390 (pttt) cc_final: 0.7635 (pttm)
REVERT: C  583 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7539 (m-80)
REVERT: C  697 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8648 (pp)
  outliers start: 34
  outliers final: 19
  residues processed: 212
  average time/residue: 0.1749
  time to fit residues: 51.9364
Evaluate side-chains
  199 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain Z residue    8 VAL
Chi-restraints excluded: chain Z residue   70 THR
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  164 THR
Chi-restraints excluded: chain Z residue  175 PHE
Chi-restraints excluded: chain Z residue  192 LEU
Chi-restraints excluded: chain B residue  472 TYR
Chi-restraints excluded: chain B residue  548 PHE
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  707 PHE
Chi-restraints excluded: chain B residue  709 GLN
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  529 THR
Chi-restraints excluded: chain C residue  540 HIS
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  592 ILE
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  639 VAL
Chi-restraints excluded: chain C residue  677 ASP
Chi-restraints excluded: chain C residue  697 LEU
Chi-restraints excluded: chain C residue  727 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
Z 151 GLN
B 581 ASN
C 540 HIS
C 562 GLN
C 581 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.112642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.091345 restraints weight = 18240.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.093716 restraints weight = 11639.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.095400 restraints weight = 8683.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7828  Z= 0.234
  Angle     :  0.655  10.186  10616  Z= 0.331
  Chirality :  0.043   0.145   1218
  Planarity :  0.004   0.031   1358
  Dihedral  :  5.679  56.900   1094
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 25.26 %
    Favored  : 69.97 %
  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: -2.17 (0.25), residues: 987
  helix: -0.80 (0.22), residues: 523
  sheet: -2.65 (0.77), residues: 42
  loop : -2.06 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 229 
 HIS   0.009   0.001   HIS C 540 
 PHE   0.046   0.002   PHE Z 197 
 TYR   0.018   0.001   TYR A 180 
 ARG   0.005   0.001   ARG A 128 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 186
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8397 (mt-10)
REVERT: A  122 MET cc_start: 0.7739 (mmm) cc_final: 0.7052 (mtp)
REVERT: A  148 LYS cc_start: 0.8780 (ptpp) cc_final: 0.8430 (mmtm)
REVERT: Z  212 TYR cc_start: 0.7934 (p90) cc_final: 0.7583 (p90)
REVERT: B  517 MET cc_start: 0.7952 (mmm) cc_final: 0.7312 (mmt)
REVERT: B  696 CYS cc_start: 0.8975 (m) cc_final: 0.8618 (m)
REVERT: B  711 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8141 (tp)
REVERT: B  733 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5905 (tt)
REVERT: C  462 ARG cc_start: 0.7985 (tmm-80) cc_final: 0.7726 (ttt-90)
REVERT: C  501 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8278 (mm-30)
REVERT: C  545 GLU cc_start: 0.7827 (mp0) cc_final: 0.7517 (mp0)
REVERT: C  552 LYS cc_start: 0.8468 (pttt) cc_final: 0.7631 (pttm)
REVERT: C  583 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7438 (m-80)
REVERT: C  586 GLU cc_start: 0.8866 (pm20) cc_final: 0.8594 (pm20)
REVERT: C  697 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8626 (pp)
  outliers start: 37
  outliers final: 23
  residues processed: 206
  average time/residue: 0.1701
  time to fit residues: 48.7445
Evaluate side-chains
  189 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain Z residue    8 VAL
Chi-restraints excluded: chain Z residue   47 VAL
Chi-restraints excluded: chain Z residue   51 ASN
Chi-restraints excluded: chain Z residue   70 THR
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  102 LEU
Chi-restraints excluded: chain Z residue  138 THR
Chi-restraints excluded: chain Z residue  164 THR
Chi-restraints excluded: chain Z residue  175 PHE
Chi-restraints excluded: chain Z residue  192 LEU
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  707 PHE
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain C residue  491 THR
Chi-restraints excluded: chain C residue  501 GLU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  529 THR
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  592 ILE
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  677 ASP
Chi-restraints excluded: chain C residue  697 LEU
Chi-restraints excluded: chain C residue  727 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0020
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 84 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
Z   9 GLN
B 581 ASN
B 636 GLN
C 494 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.115183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.094139 restraints weight = 18250.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.096639 restraints weight = 11321.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.098360 restraints weight = 8320.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7828  Z= 0.171
  Angle     :  0.622   8.873  10616  Z= 0.316
  Chirality :  0.043   0.159   1218
  Planarity :  0.003   0.032   1358
  Dihedral  :  5.094  46.925   1092
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 26.29 %
    Favored  : 69.33 %
  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: -1.88 (0.26), residues: 987
  helix: -0.56 (0.22), residues: 525
  sheet: -2.40 (0.79), residues: 42
  loop : -1.93 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 229 
 HIS   0.004   0.001   HIS C 585 
 PHE   0.033   0.002   PHE A 154 
 TYR   0.034   0.001   TYR B 647 
 ARG   0.003   0.000   ARG A  56 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 198
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: A  116 LYS cc_start: 0.8703 (mttt) cc_final: 0.8295 (mttm)
REVERT: A  123 LYS cc_start: 0.7470 (tptt) cc_final: 0.7202 (tptt)
REVERT: A  148 LYS cc_start: 0.8824 (ptpp) cc_final: 0.8532 (mmtm)
REVERT: Z  198 ASP cc_start: 0.8127 (m-30) cc_final: 0.7881 (m-30)
REVERT: Z  212 TYR cc_start: 0.7821 (p90) cc_final: 0.7500 (p90)
REVERT: B  517 MET cc_start: 0.7885 (mmm) cc_final: 0.7165 (mmt)
REVERT: B  592 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7935 (mm)
REVERT: B  597 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7646 (tt)
REVERT: B  696 CYS cc_start: 0.8938 (m) cc_final: 0.8356 (m)
REVERT: B  711 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7984 (tp)
REVERT: B  733 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5568 (tt)
REVERT: C  462 ARG cc_start: 0.8011 (tmm-80) cc_final: 0.7724 (ttt-90)
REVERT: C  473 LYS cc_start: 0.8755 (tppp) cc_final: 0.8513 (tptp)
REVERT: C  501 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8140 (mm-30)
REVERT: C  545 GLU cc_start: 0.7820 (mp0) cc_final: 0.7509 (mp0)
REVERT: C  552 LYS cc_start: 0.8407 (pttt) cc_final: 0.7515 (pttm)
REVERT: C  583 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7481 (m-80)
REVERT: C  697 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8542 (pp)
  outliers start: 34
  outliers final: 17
  residues processed: 218
  average time/residue: 0.1804
  time to fit residues: 54.2739
Evaluate side-chains
  212 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 188
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain Z residue   70 THR
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  175 PHE
Chi-restraints excluded: chain Z residue  192 LEU
Chi-restraints excluded: chain B residue  581 ASN
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  707 PHE
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain C residue  491 THR
Chi-restraints excluded: chain C residue  501 GLU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  529 THR
Chi-restraints excluded: chain C residue  540 HIS
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  592 ILE
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  677 ASP
Chi-restraints excluded: chain C residue  697 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 60 optimal weight:    0.7980
   chunk 54 optimal weight:   10.0000
   chunk 79 optimal weight:    8.9990
   chunk 90 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
Z 151 GLN
B 636 GLN
C 562 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.115271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.094207 restraints weight = 18606.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.096788 restraints weight = 11452.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.098603 restraints weight = 8377.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7828  Z= 0.178
  Angle     :  0.636  11.990  10616  Z= 0.319
  Chirality :  0.043   0.169   1218
  Planarity :  0.003   0.033   1358
  Dihedral  :  4.979  45.719   1092
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 26.03 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.73 (0.26), residues: 987
  helix: -0.46 (0.22), residues: 528
  sheet: -2.26 (0.80), residues: 42
  loop : -1.86 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 229 
 HIS   0.002   0.001   HIS C 477 
 PHE   0.022   0.002   PHE Z 118 
 TYR   0.023   0.001   TYR B 647 
 ARG   0.005   0.000   ARG A  56 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8313 (mt-10)
REVERT: A  116 LYS cc_start: 0.8734 (mttt) cc_final: 0.8365 (mttm)
REVERT: A  148 LYS cc_start: 0.8782 (ptpp) cc_final: 0.8538 (mmtm)
REVERT: Z  198 ASP cc_start: 0.8139 (m-30) cc_final: 0.7915 (m-30)
REVERT: Z  212 TYR cc_start: 0.7908 (p90) cc_final: 0.7633 (p90)
REVERT: B  517 MET cc_start: 0.7907 (mmm) cc_final: 0.7131 (mmt)
REVERT: B  592 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7853 (mm)
REVERT: B  597 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7673 (tt)
REVERT: B  696 CYS cc_start: 0.8973 (m) cc_final: 0.8353 (m)
REVERT: B  711 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7941 (tp)
REVERT: B  733 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5758 (tt)
REVERT: C  462 ARG cc_start: 0.8016 (tmm-80) cc_final: 0.7724 (ttt-90)
REVERT: C  473 LYS cc_start: 0.8781 (tppp) cc_final: 0.8523 (tttp)
REVERT: C  501 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8398 (mm-30)
REVERT: C  505 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8818 (mp)
REVERT: C  545 GLU cc_start: 0.7862 (mp0) cc_final: 0.7522 (mp0)
REVERT: C  552 LYS cc_start: 0.8374 (pttt) cc_final: 0.7538 (pttm)
REVERT: C  583 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7391 (m-80)
REVERT: C  697 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8588 (pp)
  outliers start: 37
  outliers final: 23
  residues processed: 209
  average time/residue: 0.1828
  time to fit residues: 52.7076
Evaluate side-chains
  212 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain Z residue    8 VAL
Chi-restraints excluded: chain Z residue   47 VAL
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  107 ILE
Chi-restraints excluded: chain Z residue  125 ASP
Chi-restraints excluded: chain Z residue  175 PHE
Chi-restraints excluded: chain Z residue  218 ILE
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  695 GLU
Chi-restraints excluded: chain B residue  707 PHE
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain C residue  491 THR
Chi-restraints excluded: chain C residue  501 GLU
Chi-restraints excluded: chain C residue  505 LEU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  529 THR
Chi-restraints excluded: chain C residue  540 HIS
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  581 ASN
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  592 ILE
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  639 VAL
Chi-restraints excluded: chain C residue  677 ASP
Chi-restraints excluded: chain C residue  697 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 81 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   chunk 11 optimal weight:    0.2980
   chunk 86 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0970
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0020
   overall best weight:    0.4188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.117084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.096338 restraints weight = 18391.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.098878 restraints weight = 11407.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.100662 restraints weight = 8370.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7828  Z= 0.162
  Angle     :  0.624  11.849  10616  Z= 0.314
  Chirality :  0.042   0.165   1218
  Planarity :  0.003   0.031   1358
  Dihedral  :  4.719  40.848   1092
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 27.19 %
    Favored  : 69.07 %
  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: -1.50 (0.26), residues: 987
  helix: -0.25 (0.22), residues: 529
  sheet: -1.83 (0.83), residues: 42
  loop : -1.82 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 476 
 HIS   0.002   0.000   HIS C 585 
 PHE   0.033   0.002   PHE Z 118 
 TYR   0.024   0.001   TYR B 647 
 ARG   0.004   0.000   ARG C 558 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 204
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8161 (mt-10)
REVERT: A  116 LYS cc_start: 0.8737 (mttt) cc_final: 0.8369 (mttm)
REVERT: B  517 MET cc_start: 0.8075 (mmm) cc_final: 0.7131 (mmt)
REVERT: B  597 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: B  696 CYS cc_start: 0.8849 (m) cc_final: 0.8114 (m)
REVERT: B  711 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7981 (tp)
REVERT: C  462 ARG cc_start: 0.8071 (tmm-80) cc_final: 0.7776 (ttt-90)
REVERT: C  505 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8889 (mp)
REVERT: C  506 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8316 (ttm110)
REVERT: C  545 GLU cc_start: 0.7824 (mp0) cc_final: 0.7537 (mp0)
REVERT: C  552 LYS cc_start: 0.8309 (pttt) cc_final: 0.7495 (pttm)
REVERT: C  583 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7425 (m-80)
REVERT: C  647 TYR cc_start: 0.9222 (t80) cc_final: 0.9011 (t80)
REVERT: C  697 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8476 (pp)
  outliers start: 29
  outliers final: 15
  residues processed: 220
  average time/residue: 0.1873
  time to fit residues: 56.3226
Evaluate side-chains
  202 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain Z residue    8 VAL
Chi-restraints excluded: chain Z residue   47 VAL
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  164 THR
Chi-restraints excluded: chain Z residue  175 PHE
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  695 GLU
Chi-restraints excluded: chain B residue  707 PHE
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain C residue  491 THR
Chi-restraints excluded: chain C residue  505 LEU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  529 THR
Chi-restraints excluded: chain C residue  581 ASN
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  592 ILE
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  677 ASP
Chi-restraints excluded: chain C residue  697 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 60 optimal weight:    9.9990
   chunk 97 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0770
   chunk 15 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0270
   chunk 88 optimal weight:    0.0010
   overall best weight:    0.5804

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

Flipped N/Q/H residues before XYZ refinement:
Z 140 ASN
Z 151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.117895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.097223 restraints weight = 18248.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.099771 restraints weight = 11256.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.101570 restraints weight = 8212.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7828  Z= 0.174
  Angle     :  0.676  11.454  10616  Z= 0.335
  Chirality :  0.043   0.204   1218
  Planarity :  0.003   0.031   1358
  Dihedral  :  4.679  40.017   1092
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 28.09 %
    Favored  : 68.43 %
  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: -1.40 (0.26), residues: 987
  helix: -0.19 (0.23), residues: 527
  sheet: -1.72 (0.83), residues: 42
  loop : -1.74 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 229 
 HIS   0.002   0.000   HIS B 542 
 PHE   0.034   0.002   PHE Z 118 
 TYR   0.033   0.002   TYR A 119 
 ARG   0.005   0.000   ARG A  56 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  517 MET cc_start: 0.7960 (mmm) cc_final: 0.6616 (mmt)
REVERT: B  597 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7789 (tt)
REVERT: B  696 CYS cc_start: 0.8886 (m) cc_final: 0.8550 (m)
REVERT: B  711 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8036 (tp)
REVERT: C  505 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8843 (mp)
REVERT: C  506 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8260 (ttm110)
REVERT: C  545 GLU cc_start: 0.7832 (mp0) cc_final: 0.7539 (mp0)
REVERT: C  552 LYS cc_start: 0.8221 (pttt) cc_final: 0.7448 (pttm)
REVERT: C  583 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7428 (m-80)
REVERT: C  697 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8543 (pp)
  outliers start: 27
  outliers final: 17
  residues processed: 206
  average time/residue: 0.1816
  time to fit residues: 51.6349
Evaluate side-chains
  204 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 182
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain Z residue    8 VAL
Chi-restraints excluded: chain Z residue   47 VAL
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  164 THR
Chi-restraints excluded: chain Z residue  175 PHE
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  707 PHE
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain C residue  491 THR
Chi-restraints excluded: chain C residue  505 LEU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  529 THR
Chi-restraints excluded: chain C residue  581 ASN
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  592 ILE
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  639 VAL
Chi-restraints excluded: chain C residue  677 ASP
Chi-restraints excluded: chain C residue  697 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:    0.2980
   chunk 69 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 84 optimal weight:    0.4980
   chunk 42 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
C 562 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.117895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.097300 restraints weight = 18180.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.099814 restraints weight = 11429.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.101576 restraints weight = 8406.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7828  Z= 0.182
  Angle     :  0.695  10.356  10616  Z= 0.345
  Chirality :  0.043   0.186   1218
  Planarity :  0.003   0.034   1358
  Dihedral  :  4.668  38.851   1092
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 28.48 %
    Favored  : 68.30 %
  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: -1.31 (0.26), residues: 987
  helix: -0.11 (0.23), residues: 525
  sheet: -1.87 (0.81), residues: 45
  loop : -1.67 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 229 
 HIS   0.002   0.001   HIS B 542 
 PHE   0.035   0.002   PHE Z 118 
 TYR   0.021   0.001   TYR B 647 
 ARG   0.005   0.000   ARG C 558 

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8075 (mt-10)
REVERT: A  122 MET cc_start: 0.6923 (mmm) cc_final: 0.6604 (mmm)
REVERT: B  517 MET cc_start: 0.8030 (mmm) cc_final: 0.6705 (mmt)
REVERT: B  597 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7867 (tt)
REVERT: B  696 CYS cc_start: 0.8814 (m) cc_final: 0.8499 (m)
REVERT: C  505 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8883 (mp)
REVERT: C  506 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8246 (ttm110)
REVERT: C  545 GLU cc_start: 0.7844 (mp0) cc_final: 0.7592 (mp0)
REVERT: C  552 LYS cc_start: 0.8234 (pttt) cc_final: 0.7472 (pttm)
REVERT: C  583 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7446 (m-80)
REVERT: C  668 MET cc_start: 0.7286 (mtp) cc_final: 0.6725 (ttt)
  outliers start: 25
  outliers final: 19
  residues processed: 201
  average time/residue: 0.1744
  time to fit residues: 48.7235
Evaluate side-chains
  203 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 181
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain Z residue   47 VAL
Chi-restraints excluded: chain Z residue   87 VAL
Chi-restraints excluded: chain Z residue  164 THR
Chi-restraints excluded: chain Z residue  175 PHE
Chi-restraints excluded: chain Z residue  218 ILE
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  695 GLU
Chi-restraints excluded: chain B residue  707 PHE
Chi-restraints excluded: chain C residue  491 THR
Chi-restraints excluded: chain C residue  505 LEU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  529 THR
Chi-restraints excluded: chain C residue  581 ASN
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  592 ILE
Chi-restraints excluded: chain C residue  619 TRP
Chi-restraints excluded: chain C residue  639 VAL
Chi-restraints excluded: chain C residue  677 ASP
Chi-restraints excluded: chain C residue  697 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 56 optimal weight:    0.0980
   chunk 67 optimal weight:    0.8980
   chunk 89 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
Z 151 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.118407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.097746 restraints weight = 17998.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.100275 restraints weight = 11366.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.102046 restraints weight = 8370.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.4178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7828  Z= 0.180
  Angle     :  0.713  13.259  10616  Z= 0.348
  Chirality :  0.043   0.200   1218
  Planarity :  0.003   0.035   1358
  Dihedral  :  4.594  37.669   1092
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 28.22 %
    Favored  : 68.43 %
  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: -1.26 (0.26), residues: 987
  helix: -0.09 (0.23), residues: 522
  sheet: -1.83 (0.82), residues: 45
  loop : -1.63 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 476 
 HIS   0.002   0.001   HIS B 542 
 PHE   0.035   0.002   PHE Z 118 
 TYR   0.035   0.001   TYR A 119 
 ARG   0.005   0.000   ARG C 558 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2394.83 seconds
wall clock time: 43 minutes 49.64 seconds (2629.64 seconds total)