Starting phenix.real_space_refine
on Tue Jun 17 04:54:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xn4_22267/06_2025/6xn4_22267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xn4_22267/06_2025/6xn4_22267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xn4_22267/06_2025/6xn4_22267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xn4_22267/06_2025/6xn4_22267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xn4_22267/06_2025/6xn4_22267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xn4_22267/06_2025/6xn4_22267.cif"
  }
  resolution = 3.35
  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=   0.003
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      64      5.49       5
     S      48      5.16       5
     C   12041      2.51       5
     N    3263      2.21       5
     O    3857      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 19273
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "B"
      Number of atoms: 2227
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 275, 2225
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 275, 2225
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 2272
    Chain: "F"
      Number of atoms: 1617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1617
          Classifications: {'peptide': 207}
          Link IDs: {'PTRANS': 4, 'TRANS': 202}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "H"
      Number of atoms: 1673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1673
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 5, 'TRANS': 208}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "G"
      Number of atoms: 1673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1673
          Classifications: {'peptide': 214}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 736
          Classifications: {'RNA': 35}
          Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 16, 'rna3p': 18}
    Chain: "C"
      Number of atoms: 1115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1115
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 136}
    Chain: "D"
      Number of atoms: 1089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1089
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "T"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 644
          Classifications: {'RNA': 30}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 4, 'rna3p': 25}
    Chain: "A"
      Number of atoms: 5984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 741, 5984
          Classifications: {'peptide': 741}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 730}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "J"
      Number of atoms: 2515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2515
          Classifications: {'peptide': 309}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 294}
          Chain breaks: 3
  Time building chain proxies: 11.92, per 1000 atoms: 0.62
  Number of scatterers: 19273
  At special positions: 0
  Unit cell: (109.548, 126.732, 183.654, 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      48     16.00
     P      64     15.00
     O    3857      8.00
     N    3263      7.00
     C   12041      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 405 " - pdb=" SG  CYS A 418 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 405 " - pdb=" SG  CYS A 421 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 418 " - pdb=" SG  CYS A 421 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.17
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4184

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 24 sheets defined
      40.5% alpha, 12.8% beta
      2 base pairs and 22 stacking pairs defined.
    Time for finding SS restraints: 6.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 27 through 43
    Processing helix  chain 'B' and resid 44 through 54
    Processing helix  chain 'B' and resid 163 through 171
      removed outlier: 3.582A  pdb=" N   GLU B 171 " --> pdb=" O   GLU B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 205
      removed outlier: 3.555A  pdb=" N   PHE B 203 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 227
      removed outlier: 4.073A  pdb=" N   LEU B 227 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 61
      removed outlier: 3.543A  pdb=" N   LEU F  49 " --> pdb=" O   PRO F  45 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU F  60 " --> pdb=" O   LEU F  56 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 80
    Processing helix  chain 'F' and resid 154 through 156
      No H-bonds generated for 'chain 'F' and resid 154 through 156'
    Processing helix  chain 'F' and resid 157 through 172
      removed outlier: 3.600A  pdb=" N   GLY F 168 " --> pdb=" O   ASN F 164 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 180 through 184
      removed outlier: 3.546A  pdb=" N   ARG F 183 " --> pdb=" O   HIS F 180 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 214
    Processing helix  chain 'H' and resid 45 through 61
    Processing helix  chain 'H' and resid 74 through 82
    Processing helix  chain 'H' and resid 103 through 108
    Processing helix  chain 'H' and resid 157 through 174
      removed outlier: 3.537A  pdb=" N   ASN H 164 " --> pdb=" O   LYS H 160 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS H 166 " --> pdb=" O   PHE H 162 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE H 174 " --> pdb=" O   ASP H 170 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 202 through 204
      No H-bonds generated for 'chain 'H' and resid 202 through 204'
    Processing helix  chain 'H' and resid 205 through 213
    Processing helix  chain 'G' and resid 45 through 61
      removed outlier: 3.797A  pdb=" N   LEU G  49 " --> pdb=" O   PRO G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 77 through 82
    Processing helix  chain 'G' and resid 103 through 110
    Processing helix  chain 'G' and resid 157 through 173
    Processing helix  chain 'G' and resid 204 through 213
    Processing helix  chain 'C' and resid 26 through 38
    Processing helix  chain 'C' and resid 53 through 72
      removed outlier: 3.539A  pdb=" N   ILE C  57 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL C  67 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   ARG C  70 " --> pdb=" O   LYS C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 101
      removed outlier: 3.732A  pdb=" N   GLU C 101 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 111
    Processing helix  chain 'C' and resid 112 through 124
    Processing helix  chain 'C' and resid 125 through 146
    Processing helix  chain 'D' and resid 25 through 38
    Processing helix  chain 'D' and resid 53 through 73
      removed outlier: 4.369A  pdb=" N   VAL D  67 " --> pdb=" O   LEU D  63 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG D  70 " --> pdb=" O   LYS D  66 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ASN D  73 " --> pdb=" O   ASN D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 101
      removed outlier: 3.554A  pdb=" N   ALA D  85 " --> pdb=" O   GLU D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 111
      removed outlier: 3.621A  pdb=" N   THR D 111 " --> pdb=" O   PHE D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 124
    Processing helix  chain 'D' and resid 125 through 146
      removed outlier: 3.506A  pdb=" N   TYR D 146 " --> pdb=" O   TYR D 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3 through 11
    Processing helix  chain 'A' and resid 14 through 19
      removed outlier: 3.657A  pdb=" N   LYS A  17 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE A  19 " --> pdb=" O   GLY A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 40
      removed outlier: 4.300A  pdb=" N   LYS A  38 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   SER A  39 " --> pdb=" O   ASP A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 54
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 72 through 85
      removed outlier: 4.116A  pdb=" N   THR A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR A  77 " --> pdb=" O   PHE A  73 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   GLY A  85 " --> pdb=" O   ASN A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 120
      removed outlier: 3.801A  pdb=" N   LYS A 119 " --> pdb=" O   ASN A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 168
      removed outlier: 3.522A  pdb=" N   TYR A 154 " --> pdb=" O   THR A 150 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A 165 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLN A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 173
      No H-bonds generated for 'chain 'A' and resid 171 through 173'
    Processing helix  chain 'A' and resid 174 through 186
    Processing helix  chain 'A' and resid 187 through 189
      No H-bonds generated for 'chain 'A' and resid 187 through 189'
    Processing helix  chain 'A' and resid 195 through 199
      removed outlier: 3.848A  pdb=" N   VAL A 199 " --> pdb=" O   ASN A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 224
      removed outlier: 3.597A  pdb=" N   HIS A 206 " --> pdb=" O   SER A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 263
    Processing helix  chain 'A' and resid 270 through 295
      removed outlier: 4.081A  pdb=" N   ASP A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 337
    Processing helix  chain 'A' and resid 364 through 381
    Processing helix  chain 'A' and resid 385 through 394
    Processing helix  chain 'A' and resid 418 through 430
      removed outlier: 3.878A  pdb=" N   SER A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ARG A 429 " --> pdb=" O   GLN A 425 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ASP A 430 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 3.931A  pdb=" N   SER A 467 " --> pdb=" O   LYS A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 505
      removed outlier: 3.679A  pdb=" N   GLU A 505 " --> pdb=" O   HIS A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 530
    Processing helix  chain 'A' and resid 540 through 564
      removed outlier: 3.920A  pdb=" N   THR A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE A 545 " --> pdb=" O   ARG A 541 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER A 546 " --> pdb=" O   THR A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 603
      removed outlier: 4.391A  pdb=" N   ASP A 589 " --> pdb=" O   GLN A 585 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   ILE A 592 " --> pdb=" O   LEU A 588 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL A 593 " --> pdb=" O   ASP A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 638
      removed outlier: 3.710A  pdb=" N   ASP A 637 " --> pdb=" O   ASP A 633 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 674
    Processing helix  chain 'A' and resid 674 through 682
      removed outlier: 3.522A  pdb=" N   GLU A 682 " --> pdb=" O   THR A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 701
      removed outlier: 3.654A  pdb=" N   GLY A 701 " --> pdb=" O   ASP A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 720
    Processing helix  chain 'A' and resid 727 through 739
    Processing helix  chain 'A' and resid 740 through 754
      removed outlier: 3.574A  pdb=" N   MET A 745 " --> pdb=" O   LYS A 741 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ALA A 746 " --> pdb=" O   THR A 742 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 42 through 52
      removed outlier: 3.514A  pdb=" N   THR J  46 " --> pdb=" O   HIS J  42 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 54 through 65
      removed outlier: 3.803A  pdb=" N   VAL J  62 " --> pdb=" O   PHE J  58 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 70 through 76
    Processing helix  chain 'J' and resid 127 through 138
      removed outlier: 3.684A  pdb=" N   LEU J 131 " --> pdb=" O   PRO J 127 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 151 through 155
      removed outlier: 3.637A  pdb=" N   ALA J 154 " --> pdb=" O   GLU J 151 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 165 through 167
      No H-bonds generated for 'chain 'J' and resid 165 through 167'
    Processing helix  chain 'J' and resid 209 through 229
      removed outlier: 3.650A  pdb=" N   ILE J 213 " --> pdb=" O   THR J 209 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TRP J 228 " --> pdb=" O   TYR J 224 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 286 through 301
      removed outlier: 4.047A  pdb=" N   GLN J 290 " --> pdb=" O   LYS J 286 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ARG J 292 " --> pdb=" O   ARG J 288 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   LEU J 299 " --> pdb=" O   SER J 295 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 99
      removed outlier: 3.649A  pdb=" N   PHE B  65 " --> pdb=" O   GLY B 154 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   TYR B   7 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 132
    Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 265
    Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 237
    Processing sheet with id=AA5, first strand: chain 'B' and resid 274 through 277
      removed outlier: 5.858A  pdb=" N   VAL B 284 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 94 through 96
      removed outlier: 7.675A  pdb=" N   LYS F   2 " --> pdb=" O   ALA F 198 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   THR F   8 " --> pdb=" O   ASN F 192 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   ASN F 192 " --> pdb=" O   THR F   8 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   VAL F  10 " --> pdb=" O   PHE F 190 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   PHE F 190 " --> pdb=" O   VAL F  10 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 43 through 44
    Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 123
    Processing sheet with id=AA9, first strand: chain 'H' and resid 94 through 95
      removed outlier: 3.723A  pdb=" N   PHE H 146 " --> pdb=" O   GLY H   7 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   THR H   8 " --> pdb=" O   ASN H 192 " (cutoff:3.500A)
      removed outlier: 5.579A  pdb=" N   ASN H 192 " --> pdb=" O   THR H   8 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL H  10 " --> pdb=" O   PHE H 190 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   PHE H 190 " --> pdb=" O   VAL H  10 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 43 through 44
    Processing sheet with id=AB2, first strand: chain 'H' and resid 115 through 123
    Processing sheet with id=AB3, first strand: chain 'G' and resid 94 through 95
      removed outlier: 6.447A  pdb=" N   VAL G   4 " --> pdb=" O   VAL G 195 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   VAL G 195 " --> pdb=" O   VAL G   4 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   GLU G   6 " --> pdb=" O   LEU G 193 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU G 193 " --> pdb=" O   GLU G   6 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 44
    Processing sheet with id=AB5, first strand: chain 'G' and resid 115 through 120
    Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 43
      removed outlier: 3.804A  pdb=" N   PHE C  42 " --> pdb=" O   GLN C  50 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 304 through 305
      removed outlier: 4.215A  pdb=" N   PHE A 247 " --> pdb=" O   VAL A 352 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 352 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET A 249 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   TYR A 344 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 439 through 440
    Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 475
    Processing sheet with id=AC1, first strand: chain 'A' and resid 568 through 570
      removed outlier: 3.518A  pdb=" N   ALA A 651 " --> pdb=" O   ILE A 608 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 5
    Processing sheet with id=AC3, first strand: chain 'J' and resid 196 through 198
    Processing sheet with id=AC4, first strand: chain 'J' and resid 22 through 23
      removed outlier: 6.666A  pdb=" N   LEU J 184 " --> pdb=" O   ASP J 176 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ASP J 176 " --> pdb=" O   LEU J 184 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   LEU J 186 " --> pdb=" O   LYS J 174 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLN J 173 " --> pdb=" O   ALA J  91 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'J' and resid 37 through 40
      removed outlier: 3.897A  pdb=" N   TYR J  86 " --> pdb=" O   MET J  39 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'J' and resid 314 through 315

    729 hydrogen bonds defined for protein.
    2103 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      4 hydrogen bonds
      8 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      22 stacking parallelities
  Total time for adding SS restraints: 6.08

  Time building geometry restraints manager: 5.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 6115
        1.34 -     1.48: 5333
        1.48 -     1.62: 8202
        1.62 -     1.76: 4
        1.76 -     1.89: 88
  Bond restraints: 19742
  Sorted by residual:
  bond pdb=" CA  ASN J 141 "
       pdb=" C   ASN J 141 "
    ideal  model  delta    sigma   weight residual
    1.522  1.436  0.087 1.37e-02 5.33e+03 4.00e+01
  bond pdb=" N   SER H  21 "
       pdb=" CA  SER H  21 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.15e-02 7.56e+03 1.28e+01
  bond pdb=" C   LYS J 170 "
       pdb=" N   VAL J 171 "
    ideal  model  delta    sigma   weight residual
    1.329  1.289  0.040 1.46e-02 4.69e+03 7.61e+00
  bond pdb=" CG1 ILE A 708 "
       pdb=" CD1 ILE A 708 "
    ideal  model  delta    sigma   weight residual
    1.513  1.407  0.106 3.90e-02 6.57e+02 7.45e+00
  bond pdb=" C   GLN J 259 "
       pdb=" N   PRO J 260 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.032 1.19e-02 7.06e+03 7.37e+00
  ... (remaining 19737 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.07: 26473
        4.07 -     8.15: 381
        8.15 -    12.22: 30
       12.22 -    16.30: 3
       16.30 -    20.37: 1
  Bond angle restraints: 26888
  Sorted by residual:
  angle pdb=" CA  CYS A 418 "
        pdb=" CB  CYS A 418 "
        pdb=" SG  CYS A 418 "
      ideal   model   delta    sigma   weight residual
     114.40  134.77  -20.37 2.30e+00 1.89e-01 7.84e+01
  angle pdb=" C   SER H  20 "
        pdb=" N   SER H  21 "
        pdb=" CA  SER H  21 "
      ideal   model   delta    sigma   weight residual
     123.91  136.92  -13.01 1.66e+00 3.63e-01 6.14e+01
  angle pdb=" N   ILE J  17 "
        pdb=" CA  ILE J  17 "
        pdb=" C   ILE J  17 "
      ideal   model   delta    sigma   weight residual
     113.71  107.32    6.39 9.50e-01 1.11e+00 4.53e+01
  angle pdb=" N   ILE A 341 "
        pdb=" CA  ILE A 341 "
        pdb=" C   ILE A 341 "
      ideal   model   delta    sigma   weight residual
     113.71  107.52    6.19 9.50e-01 1.11e+00 4.24e+01
  angle pdb=" N   VAL A 199 "
        pdb=" CA  VAL A 199 "
        pdb=" C   VAL A 199 "
      ideal   model   delta    sigma   weight residual
     113.10  107.33    5.77 9.70e-01 1.06e+00 3.54e+01
  ... (remaining 26883 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.63: 11568
       34.63 -    69.25: 374
       69.25 -   103.88: 38
      103.88 -   138.50: 4
      138.50 -   173.13: 2
  Dihedral angle restraints: 11986
    sinusoidal: 5486
      harmonic: 6500
  Sorted by residual:
  dihedral pdb=" CA  SER H  20 "
           pdb=" C   SER H  20 "
           pdb=" N   SER H  21 "
           pdb=" CA  SER H  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   46.16  133.84     0      5.00e+00 4.00e-02 7.16e+02
  dihedral pdb=" CA  ILE H  26 "
           pdb=" C   ILE H  26 "
           pdb=" N   GLY H  27 "
           pdb=" CA  GLY H  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  116.21   63.79     0      5.00e+00 4.00e-02 1.63e+02
  dihedral pdb=" CA  ILE G  26 "
           pdb=" C   ILE G  26 "
           pdb=" N   GLY G  27 "
           pdb=" CA  GLY G  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  120.81   59.19     0      5.00e+00 4.00e-02 1.40e+02
  ... (remaining 11983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 2711
       0.100 -    0.200: 299
       0.200 -    0.300: 33
       0.300 -    0.399: 4
       0.399 -    0.499: 3
  Chirality restraints: 3050
  Sorted by residual:
  chirality pdb=" CB  ILE A 708 "
            pdb=" CA  ILE A 708 "
            pdb=" CG1 ILE A 708 "
            pdb=" CG2 ILE A 708 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.15    0.50 2.00e-01 2.50e+01 6.23e+00
  chirality pdb=" CB  VAL B 131 "
            pdb=" CA  VAL B 131 "
            pdb=" CG1 VAL B 131 "
            pdb=" CG2 VAL B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.16   -0.47 2.00e-01 2.50e+01 5.44e+00
  chirality pdb=" C1'   A T  29 "
            pdb=" O4'   A T  29 "
            pdb=" C2'   A T  29 "
            pdb=" N9    A T  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.03    0.41 2.00e-01 2.50e+01 4.19e+00
  ... (remaining 3047 not shown)

  Planarity restraints: 3212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET H  15 "   -0.018 2.00e-02 2.50e+03   3.73e-02 1.39e+01
        pdb=" C   MET H  15 "    0.065 2.00e-02 2.50e+03
        pdb=" O   MET H  15 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   HIS H  16 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 137 "   -0.017 2.00e-02 2.50e+03   3.40e-02 1.15e+01
        pdb=" CD  GLU C 137 "    0.059 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 137 "   -0.021 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 137 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET G  15 "   -0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   MET G  15 "    0.056 2.00e-02 2.50e+03
        pdb=" O   MET G  15 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   HIS G  16 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 3209 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 1373
        2.71 -     3.26: 19283
        3.26 -     3.81: 34177
        3.81 -     4.35: 41684
        4.35 -     4.90: 68043
  Nonbonded interactions: 164560
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 128 "
            pdb=" OH  TYR B 186 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" OH  TYR B 232 "
            pdb=" O   TYR A 383 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER F  47 "
            pdb=" OP1   A R   9 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG  SER C  55 "
            pdb=" OP2   U T  22 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG  SER H  47 "
            pdb=" OP1   A R  21 "
     model   vdw
     2.243 3.040
  ... (remaining 164555 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 'C' and resid 12 through 146)
  selection = chain 'D'
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214))
  selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  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:          0.690
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     47.090
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.090
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
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      :  0.009   0.106  19745  Z= 0.409
  Angle     :  1.247  20.371  26894  Z= 0.681
  Chirality :  0.067   0.499   3050
  Planarity :  0.006   0.052   3212
  Dihedral  : 17.199 173.125   7793
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.04 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

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: -3.52 (0.15), residues: 2202
  helix: -2.11 (0.15), residues: 827
  sheet: -1.71 (0.27), residues: 323
  loop : -2.70 (0.16), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 186 
 HIS   0.009   0.002   HIS J 282 
 PHE   0.049   0.004   PHE J 255 
 TYR   0.036   0.004   TYR J 283 
 ARG   0.020   0.001   ARG D 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19668 (  733)
  hydrogen bonds       : angle       8.48547 ( 2111)
  SS BOND              : bond        0.01710 (    3)
  SS BOND              : angle       9.81106 (    6)
  covalent geometry    : bond        0.00893 (19742)
  covalent geometry    : angle       1.23804 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 2.002 
Fit side-chains
   revert: symmetry clash
REVERT: F  120 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6603 (mm-30)
REVERT: H   55 TYR cc_start: 0.8762 (t80) cc_final: 0.8487 (t80)
REVERT: A   86 MET cc_start: 0.2028 (mpp) cc_final: 0.1611 (mpp)
REVERT: A  250 MET cc_start: 0.8612 (tmm) cc_final: 0.8124 (tmm)
REVERT: A  447 MET cc_start: 0.8166 (ptt) cc_final: 0.7550 (ptt)
REVERT: A  453 MET cc_start: 0.8017 (ttm) cc_final: 0.7631 (ttm)
REVERT: A  580 MET cc_start: 0.7654 (mtm) cc_final: 0.7385 (mtm)
REVERT: J  292 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7938 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2997
  time to fit residues: 52.4624
Evaluate side-chains
  81 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 2.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 189 optimal weight:    1.9990
   chunk 170 optimal weight:    9.9990
   chunk 94 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 176 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 131 optimal weight:   40.0000
   chunk 204 optimal weight:    5.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
H 124 ASN
H 192 ASN
A 251 ASN
A 355 ASN
J  74 ASN
J  92 GLN
J 111 ASN
J 141 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.081566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.064350 restraints weight = 94611.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 4.68
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  19745  Z= 0.148
  Angle     :  0.693  19.198  26894  Z= 0.368
  Chirality :  0.043   0.224   3050
  Planarity :  0.004   0.054   3212
  Dihedral  : 16.326 159.880   3392
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.13 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.92 %
    Favored  : 92.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.70 (0.16), residues: 2202
  helix: -0.97 (0.16), residues: 849
  sheet: -1.58 (0.24), residues: 384
  loop : -2.61 (0.18), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 334 
 HIS   0.004   0.001   HIS H  16 
 PHE   0.039   0.001   PHE A  36 
 TYR   0.018   0.002   TYR B 232 
 ARG   0.005   0.001   ARG J 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04360 (  733)
  hydrogen bonds       : angle       5.91392 ( 2111)
  SS BOND              : bond        0.01925 (    3)
  SS BOND              : angle       9.85328 (    6)
  covalent geometry    : bond        0.00310 (19742)
  covalent geometry    : angle       0.67763 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 2.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.2158 (mpp) cc_final: 0.1607 (mpp)
REVERT: A  250 MET cc_start: 0.8645 (tmm) cc_final: 0.8131 (tmm)
REVERT: A  453 MET cc_start: 0.8233 (ttm) cc_final: 0.7926 (ttt)
  outliers start: 11
  outliers final: 4
  residues processed: 116
  average time/residue: 0.3150
  time to fit residues: 58.4195
Evaluate side-chains
  87 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 2.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 MET
Chi-restraints excluded: chain G residue  204 LYS
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain A residue    8 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 162 optimal weight:    8.9990
   chunk 169 optimal weight:    0.8980
   chunk 103 optimal weight:    9.9990
   chunk 22 optimal weight:    0.2980
   chunk 52 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 183 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   overall best weight:    2.8386

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

Flipped N/Q/H residues before XYZ refinement:
C  39 HIS
A 355 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.080321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.064335 restraints weight = 120198.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 4.33
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  19745  Z= 0.193
  Angle     :  0.681  19.217  26894  Z= 0.361
  Chirality :  0.044   0.250   3050
  Planarity :  0.004   0.052   3212
  Dihedral  : 16.233 163.091   3392
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.45 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 10.89 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.32 %

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: -2.26 (0.17), residues: 2202
  helix: -0.44 (0.17), residues: 852
  sheet: -1.44 (0.25), residues: 359
  loop : -2.47 (0.18), residues: 991

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 186 
 HIS   0.005   0.001   HIS H  16 
 PHE   0.025   0.002   PHE A  36 
 TYR   0.019   0.002   TYR J  71 
 ARG   0.005   0.001   ARG D 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  733)
  hydrogen bonds       : angle       5.60191 ( 2111)
  SS BOND              : bond        0.02193 (    3)
  SS BOND              : angle      10.00202 (    6)
  covalent geometry    : bond        0.00413 (19742)
  covalent geometry    : angle       0.66400 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 2.070 
Fit side-chains
   revert: symmetry clash
REVERT: G   53 MET cc_start: 0.8599 (mtp) cc_final: 0.8365 (ttt)
REVERT: A   86 MET cc_start: 0.2430 (mpp) cc_final: 0.1929 (mpp)
REVERT: A  250 MET cc_start: 0.8532 (tmm) cc_final: 0.8264 (tmm)
REVERT: A  580 MET cc_start: 0.8285 (mtm) cc_final: 0.8080 (mtm)
  outliers start: 15
  outliers final: 6
  residues processed: 96
  average time/residue: 0.2731
  time to fit residues: 44.7739
Evaluate side-chains
  87 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 2.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue  202 PHE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain A residue    8 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 190 optimal weight:    5.9990
   chunk 135 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 132 GLN
F 131 ASN
** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 HIS
** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 282 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.078261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.060743 restraints weight = 94504.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 4.44
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  19745  Z= 0.308
  Angle     :  0.778  19.678  26894  Z= 0.409
  Chirality :  0.047   0.305   3050
  Planarity :  0.005   0.055   3212
  Dihedral  : 16.568 163.290   3392
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.22 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.01 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.25 (0.17), residues: 2202
  helix: -0.29 (0.17), residues: 847
  sheet: -1.60 (0.26), residues: 348
  loop : -2.52 (0.18), residues: 1007

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 186 
 HIS   0.007   0.001   HIS H  16 
 PHE   0.021   0.002   PHE G  96 
 TYR   0.021   0.002   TYR J 283 
 ARG   0.006   0.001   ARG D  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04533 (  733)
  hydrogen bonds       : angle       5.72810 ( 2111)
  SS BOND              : bond        0.02506 (    3)
  SS BOND              : angle      10.36675 (    6)
  covalent geometry    : bond        0.00668 (19742)
  covalent geometry    : angle       0.76288 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 2.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 LYS cc_start: 0.8171 (pttm) cc_final: 0.7596 (mtpt)
REVERT: C   39 HIS cc_start: 0.7512 (m90) cc_final: 0.6976 (m90)
REVERT: C  109 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7678 (tm-30)
REVERT: A    1 MET cc_start: 0.6593 (ttm) cc_final: 0.6334 (ttt)
REVERT: A  250 MET cc_start: 0.8679 (tmm) cc_final: 0.8208 (tmm)
REVERT: J  289 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.8020 (p0)
  outliers start: 37
  outliers final: 17
  residues processed: 114
  average time/residue: 0.2615
  time to fit residues: 50.8607
Evaluate side-chains
  94 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 2.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   52 LYS
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  210 GLU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  202 PHE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain J residue  140 LEU
Chi-restraints excluded: chain J residue  289 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 156 optimal weight:    1.9990
   chunk 179 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 216 optimal weight:    1.9990
   chunk 152 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 196 optimal weight:    0.4980
   chunk 64 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 118 optimal weight:   10.0000
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 ASN
A 359 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.081395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.063890 restraints weight = 100940.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 4.78
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  19745  Z= 0.128
  Angle     :  0.630  18.679  26894  Z= 0.331
  Chirality :  0.042   0.211   3050
  Planarity :  0.003   0.057   3212
  Dihedral  : 15.901 157.470   3392
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.81 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.66 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

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: -1.97 (0.17), residues: 2202
  helix: -0.02 (0.18), residues: 850
  sheet: -1.40 (0.26), residues: 355
  loop : -2.45 (0.18), residues: 997

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A  55 
 PHE   0.013   0.001   PHE A  36 
 TYR   0.015   0.001   TYR A  77 
 ARG   0.007   0.000   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  733)
  hydrogen bonds       : angle       5.27490 ( 2111)
  SS BOND              : bond        0.02315 (    3)
  SS BOND              : angle       9.88902 (    6)
  covalent geometry    : bond        0.00271 (19742)
  covalent geometry    : angle       0.61265 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 2.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   39 HIS cc_start: 0.7445 (m90) cc_final: 0.7210 (m90)
REVERT: C  109 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7663 (tm-30)
REVERT: A    1 MET cc_start: 0.6642 (ttm) cc_final: 0.6430 (ttt)
REVERT: A   86 MET cc_start: 0.2565 (mtt) cc_final: 0.2256 (mpp)
REVERT: A  142 PRO cc_start: 0.5080 (Cg_exo) cc_final: 0.4801 (Cg_endo)
REVERT: A  250 MET cc_start: 0.8564 (tmm) cc_final: 0.8153 (tmm)
  outliers start: 30
  outliers final: 15
  residues processed: 113
  average time/residue: 0.2582
  time to fit residues: 50.1520
Evaluate side-chains
  100 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 2.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   52 LYS
Chi-restraints excluded: chain H residue  210 GLU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  202 PHE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain J residue   84 VAL
Chi-restraints excluded: chain J residue  140 LEU
Chi-restraints excluded: chain J residue  254 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 176 optimal weight:   10.0000
   chunk 140 optimal weight:    4.9990
   chunk 118 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 90 optimal weight:    8.9990
   chunk 177 optimal weight:    5.9990
   chunk 161 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
F  16 HIS
F 121 ASN
** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.077729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.060285 restraints weight = 94773.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 4.29
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.100  19745  Z= 0.339
  Angle     :  0.797  19.349  26894  Z= 0.416
  Chirality :  0.048   0.305   3050
  Planarity :  0.005   0.058   3212
  Dihedral  : 16.530 162.520   3392
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.08 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.87 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.15 (0.17), residues: 2202
  helix: -0.16 (0.17), residues: 848
  sheet: -1.58 (0.26), residues: 346
  loop : -2.51 (0.18), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 186 
 HIS   0.005   0.001   HIS G 180 
 PHE   0.023   0.002   PHE F 162 
 TYR   0.021   0.002   TYR J 283 
 ARG   0.007   0.001   ARG D  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04523 (  733)
  hydrogen bonds       : angle       5.67004 ( 2111)
  SS BOND              : bond        0.02586 (    3)
  SS BOND              : angle      10.33435 (    6)
  covalent geometry    : bond        0.00735 (19742)
  covalent geometry    : angle       0.78236 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 85
  time to evaluate  : 2.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 LYS cc_start: 0.8179 (pttm) cc_final: 0.7527 (ttpt)
REVERT: G   53 MET cc_start: 0.8718 (mtp) cc_final: 0.8487 (ttt)
REVERT: C   39 HIS cc_start: 0.7463 (m90) cc_final: 0.6948 (m90)
REVERT: C  109 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7781 (tm-30)
REVERT: A    1 MET cc_start: 0.6649 (ttm) cc_final: 0.6362 (ttt)
REVERT: A  142 PRO cc_start: 0.5202 (Cg_exo) cc_final: 0.4919 (Cg_endo)
REVERT: A  250 MET cc_start: 0.8691 (tmm) cc_final: 0.8211 (tmm)
REVERT: J  289 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7991 (p0)
  outliers start: 42
  outliers final: 27
  residues processed: 119
  average time/residue: 0.2803
  time to fit residues: 55.4879
Evaluate side-chains
  107 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 2.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue    8 THR
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   52 LYS
Chi-restraints excluded: chain H residue   53 MET
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  210 GLU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  202 PHE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  453 MET
Chi-restraints excluded: chain J residue   84 VAL
Chi-restraints excluded: chain J residue  140 LEU
Chi-restraints excluded: chain J residue  254 THR
Chi-restraints excluded: chain J residue  289 ASP
Chi-restraints excluded: chain J residue  347 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 182 optimal weight:    0.8980
   chunk 146 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 158 optimal weight:    7.9990
   chunk 164 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.080348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.063146 restraints weight = 92141.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 4.62
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  19745  Z= 0.143
  Angle     :  0.639  18.527  26894  Z= 0.334
  Chirality :  0.043   0.219   3050
  Planarity :  0.003   0.052   3212
  Dihedral  : 15.899 158.439   3392
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.99 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.06 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.87 (0.17), residues: 2202
  helix:  0.14 (0.18), residues: 848
  sheet: -1.49 (0.26), residues: 340
  loop : -2.39 (0.18), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A  55 
 PHE   0.012   0.001   PHE J 255 
 TYR   0.014   0.001   TYR F  55 
 ARG   0.005   0.000   ARG J 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  733)
  hydrogen bonds       : angle       5.24989 ( 2111)
  SS BOND              : bond        0.02420 (    3)
  SS BOND              : angle       9.95589 (    6)
  covalent geometry    : bond        0.00304 (19742)
  covalent geometry    : angle       0.62154 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 93
  time to evaluate  : 2.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   53 MET cc_start: 0.8562 (mtp) cc_final: 0.8286 (ttt)
REVERT: C   39 HIS cc_start: 0.7431 (m90) cc_final: 0.6960 (m90)
REVERT: C   62 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7436 (mp0)
REVERT: C  109 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7801 (tm-30)
REVERT: A    1 MET cc_start: 0.6991 (ttm) cc_final: 0.6785 (ttt)
REVERT: A  142 PRO cc_start: 0.4977 (Cg_exo) cc_final: 0.4718 (Cg_endo)
REVERT: A  250 MET cc_start: 0.8721 (tmm) cc_final: 0.8186 (tmm)
  outliers start: 31
  outliers final: 25
  residues processed: 118
  average time/residue: 0.2793
  time to fit residues: 55.8146
Evaluate side-chains
  112 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 2.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   52 LYS
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  210 GLU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  202 PHE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  580 MET
Chi-restraints excluded: chain J residue   50 LEU
Chi-restraints excluded: chain J residue   84 VAL
Chi-restraints excluded: chain J residue  140 LEU
Chi-restraints excluded: chain J residue  254 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 184 optimal weight:   10.0000
   chunk 194 optimal weight:    4.9990
   chunk 128 optimal weight:   20.0000
   chunk 158 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 220 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.081421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.064036 restraints weight = 95450.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 4.63
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  19745  Z= 0.125
  Angle     :  0.619  18.391  26894  Z= 0.321
  Chirality :  0.042   0.196   3050
  Planarity :  0.003   0.051   3212
  Dihedral  : 15.690 160.033   3392
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.86 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.06 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.74 (0.17), residues: 2202
  helix:  0.30 (0.18), residues: 853
  sheet: -1.50 (0.25), residues: 362
  loop : -2.35 (0.18), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A  55 
 PHE   0.013   0.001   PHE A 579 
 TYR   0.017   0.001   TYR H  55 
 ARG   0.004   0.000   ARG J 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03531 (  733)
  hydrogen bonds       : angle       5.05533 ( 2111)
  SS BOND              : bond        0.02317 (    3)
  SS BOND              : angle       9.82181 (    6)
  covalent geometry    : bond        0.00266 (19742)
  covalent geometry    : angle       0.60163 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 2.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   53 MET cc_start: 0.8572 (mtp) cc_final: 0.8275 (ttt)
REVERT: C   39 HIS cc_start: 0.7747 (m90) cc_final: 0.7187 (m90)
REVERT: D  121 MET cc_start: 0.8597 (mmp) cc_final: 0.8383 (mmp)
REVERT: A  142 PRO cc_start: 0.5281 (Cg_exo) cc_final: 0.5024 (Cg_endo)
REVERT: A  250 MET cc_start: 0.8739 (tmm) cc_final: 0.8219 (tmm)
REVERT: J  277 VAL cc_start: 0.8731 (t) cc_final: 0.8509 (m)
  outliers start: 34
  outliers final: 28
  residues processed: 123
  average time/residue: 0.2724
  time to fit residues: 56.5451
Evaluate side-chains
  115 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 2.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   52 LYS
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  210 GLU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue   44 ILE
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  202 PHE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  580 MET
Chi-restraints excluded: chain J residue   50 LEU
Chi-restraints excluded: chain J residue   84 VAL
Chi-restraints excluded: chain J residue  254 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 188 optimal weight:    0.0980
   chunk 217 optimal weight:    9.9990
   chunk 154 optimal weight:    3.9990
   chunk 157 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 149 optimal weight:    4.9990
   chunk 155 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.080991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.064224 restraints weight = 136646.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 5.00
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  19745  Z= 0.144
  Angle     :  0.634  18.463  26894  Z= 0.329
  Chirality :  0.042   0.193   3050
  Planarity :  0.003   0.049   3212
  Dihedral  : 15.729 160.905   3392
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.58 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.52 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.68 (0.18), residues: 2202
  helix:  0.35 (0.18), residues: 857
  sheet: -1.47 (0.25), residues: 364
  loop : -2.33 (0.19), residues: 981

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 186 
 HIS   0.003   0.001   HIS J 282 
 PHE   0.022   0.001   PHE C  42 
 TYR   0.013   0.001   TYR B 257 
 ARG   0.005   0.000   ARG C  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03549 (  733)
  hydrogen bonds       : angle       5.08847 ( 2111)
  SS BOND              : bond        0.02372 (    3)
  SS BOND              : angle       9.91748 (    6)
  covalent geometry    : bond        0.00310 (19742)
  covalent geometry    : angle       0.61669 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 93
  time to evaluate  : 1.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   53 MET cc_start: 0.8593 (mtp) cc_final: 0.8292 (ttt)
REVERT: C   39 HIS cc_start: 0.7899 (m90) cc_final: 0.7339 (m90)
REVERT: A   86 MET cc_start: 0.1986 (mpp) cc_final: 0.1764 (mpp)
REVERT: A  142 PRO cc_start: 0.5420 (Cg_exo) cc_final: 0.5152 (Cg_endo)
REVERT: A  250 MET cc_start: 0.8601 (tmm) cc_final: 0.8215 (tmm)
REVERT: J  277 VAL cc_start: 0.8732 (t) cc_final: 0.8499 (m)
  outliers start: 32
  outliers final: 27
  residues processed: 122
  average time/residue: 0.2802
  time to fit residues: 57.3295
Evaluate side-chains
  116 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 2.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   52 LYS
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain H residue  210 GLU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  202 PHE
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  580 MET
Chi-restraints excluded: chain J residue   84 VAL
Chi-restraints excluded: chain J residue  254 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 186 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 164 optimal weight:    6.9990
   chunk 125 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 132 optimal weight:   30.0000
   chunk 207 optimal weight:    9.9990
   chunk 204 optimal weight:    0.1980
   chunk 94 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.081900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.065783 restraints weight = 121110.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 4.75
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  19745  Z= 0.121
  Angle     :  0.615  18.246  26894  Z= 0.318
  Chirality :  0.041   0.182   3050
  Planarity :  0.003   0.049   3212
  Dihedral  : 15.582 160.010   3392
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.67 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.57 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.60 (0.18), residues: 2202
  helix:  0.44 (0.18), residues: 851
  sheet: -1.45 (0.25), residues: 364
  loop : -2.29 (0.19), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 186 
 HIS   0.003   0.001   HIS J 155 
 PHE   0.011   0.001   PHE A 579 
 TYR   0.015   0.001   TYR H  55 
 ARG   0.005   0.000   ARG C  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  733)
  hydrogen bonds       : angle       4.98435 ( 2111)
  SS BOND              : bond        0.02304 (    3)
  SS BOND              : angle       9.74870 (    6)
  covalent geometry    : bond        0.00261 (19742)
  covalent geometry    : angle       0.59778 (26888)

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

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

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4404 Ramachandran restraints generated.
    2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 2.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   53 MET cc_start: 0.8546 (mtp) cc_final: 0.8237 (ttt)
REVERT: C   39 HIS cc_start: 0.7938 (m90) cc_final: 0.7387 (m90)
REVERT: A  142 PRO cc_start: 0.5363 (Cg_exo) cc_final: 0.5116 (Cg_endo)
REVERT: A  250 MET cc_start: 0.8627 (tmm) cc_final: 0.8229 (tmm)
REVERT: J  277 VAL cc_start: 0.8686 (t) cc_final: 0.8439 (m)
  outliers start: 30
  outliers final: 27
  residues processed: 117
  average time/residue: 0.2822
  time to fit residues: 54.9387
Evaluate side-chains
  117 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 1.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain F residue   13 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   52 LYS
Chi-restraints excluded: chain H residue  195 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  202 PHE
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  580 MET
Chi-restraints excluded: chain J residue   50 LEU
Chi-restraints excluded: chain J residue   84 VAL
Chi-restraints excluded: chain J residue  140 LEU
Chi-restraints excluded: chain J residue  254 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 225
   random chunks:
   chunk 188 optimal weight:    0.0980
   chunk 108 optimal weight:    4.9990
   chunk 215 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 141 optimal weight:   20.0000
   chunk 56 optimal weight:    3.9990
   chunk 40 optimal weight:    0.4980
   chunk 212 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A   5 ASN
** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.081745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.064119 restraints weight = 94488.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 4.86
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  19745  Z= 0.128
  Angle     :  0.615  18.309  26894  Z= 0.319
  Chirality :  0.041   0.180   3050
  Planarity :  0.003   0.049   3212
  Dihedral  : 15.586 160.823   3392
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.54 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.68 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.37 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.58 (0.18), residues: 2202
  helix:  0.43 (0.18), residues: 864
  sheet: -1.43 (0.25), residues: 366
  loop : -2.28 (0.19), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 186 
 HIS   0.004   0.001   HIS H  16 
 PHE   0.014   0.001   PHE J  58 
 TYR   0.013   0.001   TYR F  55 
 ARG   0.005   0.000   ARG C  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  733)
  hydrogen bonds       : angle       4.96669 ( 2111)
  SS BOND              : bond        0.02342 (    3)
  SS BOND              : angle       9.80797 (    6)
  covalent geometry    : bond        0.00276 (19742)
  covalent geometry    : angle       0.59706 (26888)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8513.02 seconds
wall clock time: 147 minutes 37.96 seconds (8857.96 seconds total)