Starting phenix.real_space_refine
on Thu Jul 31 00:32:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pz2_18035/07_2025/8pz2_18035.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pz2_18035/07_2025/8pz2_18035.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pz2_18035/07_2025/8pz2_18035.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pz2_18035/07_2025/8pz2_18035.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pz2_18035/07_2025/8pz2_18035.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pz2_18035/07_2025/8pz2_18035.cif"
  }
  resolution = 4.2
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    8240      2.51       5
     N    2258      2.21       5
     O    2579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13121
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 783, 6188
          Classifications: {'peptide': 783}
          Link IDs: {'PTRANS': 29, 'TRANS': 753}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "B"
      Number of atoms: 2777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2777
          Classifications: {'peptide': 369}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 357}
    Chain: "C"
      Number of atoms: 440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 440
          Classifications: {'peptide': 61}
          Link IDs: {'PTRANS': 6, 'TRANS': 54}
    Chain: "D"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1760
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 693
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "F"
      Number of atoms: 1263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 158, 1263
          Classifications: {'peptide': 158}
          Link IDs: {'PTRANS': 2, 'TRANS': 155}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
  Time building chain proxies: 8.23, per 1000 atoms: 0.63
  Number of scatterers: 13121
  At special positions: 0
  Unit cell: (138.45, 101.53, 125.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    2579      8.00
     N    2258      7.00
     C    8240      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.07
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3086

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 20 sheets defined
      29.2% alpha, 25.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 69
      removed outlier: 4.196A  pdb=" N   ASN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 117
      removed outlier: 3.581A  pdb=" N   GLN A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 145
      removed outlier: 3.619A  pdb=" N   ILE A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 4.055A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 233
      removed outlier: 3.609A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A 216 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG A 233 " --> pdb=" O   TYR A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.642A  pdb=" N   ILE A 284 " --> pdb=" O   HIS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 316
      removed outlier: 3.843A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 367
    Processing helix  chain 'A' and resid 378 through 392
      removed outlier: 4.102A  pdb=" N   ASP A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 392 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
    Processing helix  chain 'A' and resid 542 through 553
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 726 through 731
      removed outlier: 5.361A  pdb=" N   ASN A 731 " --> pdb=" O   LYS A 728 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 243
    Processing helix  chain 'C' and resid 39 through 44
      removed outlier: 3.597A  pdb=" N   LEU C  42 " --> pdb=" O   GLU C  39 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU C  43 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'D' and resid 31 through 46
      removed outlier: 3.570A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 4.382A  pdb=" N   THR D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
      removed outlier: 3.562A  pdb=" N   VAL D  71 " --> pdb=" O   TYR D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 99
      removed outlier: 4.247A  pdb=" N   ARG D  97 " --> pdb=" O   ASP D  93 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU D  98 " --> pdb=" O   ARG D  94 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASN D  99 " --> pdb=" O   PHE D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 121
    Processing helix  chain 'D' and resid 124 through 129
      removed outlier: 3.617A  pdb=" N   PHE D 128 " --> pdb=" O   LEU D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 154
      removed outlier: 3.701A  pdb=" N   ASP D 146 " --> pdb=" O   ALA D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 189
    Processing helix  chain 'D' and resid 190 through 205
      removed outlier: 3.548A  pdb=" N   VAL D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 224
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 4.996A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   VAL D 234 " --> pdb=" O   GLN D 230 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 46
      removed outlier: 3.676A  pdb=" N   LYS E  45 " --> pdb=" O   ASN E  41 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ILE E  46 " --> pdb=" O   ASP E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'F' and resid 39 through 49
      removed outlier: 4.115A  pdb=" N   GLN F  47 " --> pdb=" O   ASP F  43 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL F  49 " --> pdb=" O   LEU F  45 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 57
      removed outlier: 3.860A  pdb=" N   GLN F  55 " --> pdb=" O   ASN F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 88
      removed outlier: 3.597A  pdb=" N   MET F  76 " --> pdb=" O   GLU F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 105
      removed outlier: 3.704A  pdb=" N   LEU F  96 " --> pdb=" O   SER F  92 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 124 through 150
      removed outlier: 3.680A  pdb=" N   ILE F 137 " --> pdb=" O   ARG F 133 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ARG F 142 " --> pdb=" O   ILE F 138 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASN F 143 " --> pdb=" O   SER F 139 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ARG F 147 " --> pdb=" O   ASN F 143 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG F 148 " --> pdb=" O   ASN F 144 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 164
    Processing helix  chain 'F' and resid 396 through 420
      removed outlier: 3.678A  pdb=" N   ALA F 419 " --> pdb=" O   GLN F 415 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER F 420 " --> pdb=" O   GLU F 416 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31
      removed outlier: 6.735A  pdb=" N   HIS A  30 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   VAL A  88 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASP A  74 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 6.386A  pdb=" N   VAL A 163 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   SER A  96 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181
      removed outlier: 4.668A  pdb=" N   ILE A 177 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   VAL A 256 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   GLN A 179 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   VAL A 258 " --> pdb=" O   GLN A 179 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ASN A 181 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   ILE A 260 " --> pdb=" O   ASN A 181 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLY A 253 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   LEU A 247 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   TYR A 255 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   VAL A 245 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   THR A 257 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   THR A 243 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASN A 259 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ASN A 239 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 268
      removed outlier: 6.804A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268
      removed outlier: 6.804A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   THR A 334 " --> pdb=" O   ASN A 329 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU A 327 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 355
      removed outlier: 5.994A  pdb=" N   VAL A 412 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A 414 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 426
    Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 426
      removed outlier: 3.615A  pdb=" N   PHE A 490 " --> pdb=" O   GLY A 510 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLY A 510 " --> pdb=" O   PHE A 490 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674
      removed outlier: 5.461A  pdb=" N   ASP A 704 " --> pdb=" O   ALA A 672 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   TYR A 674 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   SER A 702 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 49
      removed outlier: 6.890A  pdb=" N   SER B 389 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   SER B  49 " --> pdb=" O   VAL B 387 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL B 387 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 67
      removed outlier: 3.547A  pdb=" N   ALA B  66 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118
      removed outlier: 6.147A  pdb=" N   VAL B 131 " --> pdb=" O   GLN B 144 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLN B 144 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ALA B 133 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158
    Processing sheet with id=AB5, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.746A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.584A  pdb=" N   VAL B 252 " --> pdb=" O   PHE B 259 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 286 through 291
      removed outlier: 5.154A  pdb=" N   ASP B 288 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL B 299 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333
      removed outlier: 3.781A  pdb=" N   ALA B 358 " --> pdb=" O   TRP B 348 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33
      removed outlier: 4.154A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33
      removed outlier: 6.523A  pdb=" N   THR E  90 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ASN E 106 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   THR E  92 " --> pdb=" O   ILE E 104 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   ILE E 104 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   THR E  94 " --> pdb=" O   THR E 102 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 38
      removed outlier: 3.905A  pdb=" N   VAL F  32 " --> pdb=" O   GLY F  35 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   VAL F  31 " --> pdb=" O   LYS F 424 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS F 424 " --> pdb=" O   VAL F  31 " (cutoff:3.500A)

    587 hydrogen bonds defined for protein.
    1620 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.39

  Time building geometry restraints manager: 3.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4428
        1.34 -     1.46: 2664
        1.46 -     1.58: 6210
        1.58 -     1.69: 0
        1.69 -     1.81: 83
  Bond restraints: 13385
  Sorted by residual:
  bond pdb=" CB  PHE A 395 "
       pdb=" CG  PHE A 395 "
    ideal  model  delta    sigma   weight residual
    1.502  1.468  0.034 2.30e-02 1.89e+03 2.15e+00
  bond pdb=" CB  ASP A 740 "
       pdb=" CG  ASP A 740 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.75e+00
  bond pdb=" CG  LEU A 365 "
       pdb=" CD2 LEU A 365 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.68e+00
  bond pdb=" CG  ARG B 195 "
       pdb=" CD  ARG B 195 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" CG  LEU B 261 "
       pdb=" CD2 LEU B 261 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.65e+00
  ... (remaining 13380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 17641
        1.81 -     3.62: 467
        3.62 -     5.42: 62
        5.42 -     7.23: 3
        7.23 -     9.04: 2
  Bond angle restraints: 18175
  Sorted by residual:
  angle pdb=" N   ALA C  54 "
        pdb=" CA  ALA C  54 "
        pdb=" C   ALA C  54 "
      ideal   model   delta    sigma   weight residual
     109.15  113.73   -4.58 1.44e+00 4.82e-01 1.01e+01
  angle pdb=" C   VAL A 532 "
        pdb=" N   HIS A 533 "
        pdb=" CA  HIS A 533 "
      ideal   model   delta    sigma   weight residual
     122.62  117.84    4.78 1.56e+00 4.11e-01 9.39e+00
  angle pdb=" C   THR A 479 "
        pdb=" N   VAL A 480 "
        pdb=" CA  VAL A 480 "
      ideal   model   delta    sigma   weight residual
     121.97  116.74    5.23 1.80e+00 3.09e-01 8.45e+00
  angle pdb=" N   GLY A 429 "
        pdb=" CA  GLY A 429 "
        pdb=" C   GLY A 429 "
      ideal   model   delta    sigma   weight residual
     110.63  114.70   -4.07 1.43e+00 4.89e-01 8.10e+00
  angle pdb=" CB  LEU B 261 "
        pdb=" CG  LEU B 261 "
        pdb=" CD2 LEU B 261 "
      ideal   model   delta    sigma   weight residual
     110.70  102.51    8.19 3.00e+00 1.11e-01 7.46e+00
  ... (remaining 18170 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 7162
       17.85 -    35.70: 655
       35.70 -    53.55: 118
       53.55 -    71.40: 17
       71.40 -    89.25: 21
  Dihedral angle restraints: 7973
    sinusoidal: 3135
      harmonic: 4838
  Sorted by residual:
  dihedral pdb=" CA  SER B 191 "
           pdb=" C   SER B 191 "
           pdb=" N   LEU B 192 "
           pdb=" CA  LEU B 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.82   26.18     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  THR B 386 "
           pdb=" C   THR B 386 "
           pdb=" N   VAL B 387 "
           pdb=" CA  VAL B 387 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.21  -23.79     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  VAL A 480 "
           pdb=" C   VAL A 480 "
           pdb=" N   ASP A 481 "
           pdb=" CA  ASP A 481 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.67   22.33     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 7970 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1431
       0.047 -    0.094: 444
       0.094 -    0.140: 108
       0.140 -    0.187: 8
       0.187 -    0.234: 4
  Chirality restraints: 1995
  Sorted by residual:
  chirality pdb=" CA  PHE A 394 "
            pdb=" N   PHE A 394 "
            pdb=" C   PHE A 394 "
            pdb=" CB  PHE A 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  PHE A 586 "
            pdb=" N   PHE A 586 "
            pdb=" C   PHE A 586 "
            pdb=" CB  PHE A 586 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  VAL A 364 "
            pdb=" CA  VAL A 364 "
            pdb=" CG1 VAL A 364 "
            pdb=" CG2 VAL A 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1992 not shown)

  Planarity restraints: 2399
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN F  78 "   -0.012 2.00e-02 2.50e+03   2.41e-02 5.80e+00
        pdb=" C   GLN F  78 "    0.042 2.00e-02 2.50e+03
        pdb=" O   GLN F  78 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE F  79 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  30 "   -0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO D  31 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO D  31 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D  31 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 206 "   -0.015 2.00e-02 2.50e+03   1.29e-02 4.19e+00
        pdb=" CG  TRP A 206 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 206 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 206 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 206 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 206 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 206 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2396 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 183
        2.65 -     3.21: 12553
        3.21 -     3.78: 19161
        3.78 -     4.34: 25300
        4.34 -     4.90: 42449
  Nonbonded interactions: 99646
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E  94 "
            pdb=" OD1 ASN E 103 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" NE2 GLN A 384 "
            pdb=" OE1 GLU A 521 "
     model   vdw
     2.170 3.120
  nonbonded pdb=" O   GLY F  44 "
            pdb=" OG  SER F  48 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   TYR A 548 "
            pdb=" OG  SER A 551 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OH  TYR A 608 "
            pdb=" OE2 GLU A 650 "
     model   vdw
     2.229 3.040
  ... (remaining 99641 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     31.870
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
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      :  0.006   0.049  13385  Z= 0.281
  Angle     :  0.698   9.039  18175  Z= 0.382
  Chirality :  0.048   0.234   1995
  Planarity :  0.005   0.056   2399
  Dihedral  : 14.675  89.251   4887
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.28 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.20), residues: 1662
  helix:  1.29 (0.25), residues: 420
  sheet: -0.44 (0.25), residues: 392
  loop : -1.84 (0.20), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 206 
 HIS   0.010   0.002   HIS B 347 
 PHE   0.034   0.002   PHE A 586 
 TYR   0.028   0.002   TYR E  37 
 ARG   0.006   0.000   ARG B 195 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12188 (  579)
  hydrogen bonds       : angle       5.83918 ( 1620)
  covalent geometry    : bond        0.00635 (13385)
  covalent geometry    : angle       0.69762 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A  280 HIS cc_start: 0.7408 (m-70) cc_final: 0.7128 (m-70)
REVERT: A  667 THR cc_start: 0.8460 (t) cc_final: 0.8225 (m)
REVERT: A  780 LEU cc_start: 0.8905 (mt) cc_final: 0.8268 (tt)
REVERT: D   52 ILE cc_start: 0.9275 (mt) cc_final: 0.8749 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 180
  average time/residue: 0.2362
  time to fit residues: 63.5576
Evaluate side-chains
  140 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 138 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 128 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 148 optimal weight:    0.0370
   overall best weight:    1.7664

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 561 GLN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** 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 = 0.3413 r_free = 0.3413 target = 0.111729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.086587 restraints weight = 26509.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.085811 restraints weight = 25848.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.086552 restraints weight = 25205.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13385  Z= 0.135
  Angle     :  0.544   7.851  18175  Z= 0.294
  Chirality :  0.043   0.149   1995
  Planarity :  0.004   0.052   2399
  Dihedral  :  4.473  25.195   1839
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.73 %
    Favored  : 94.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.20), residues: 1662
  helix:  1.50 (0.25), residues: 429
  sheet: -0.50 (0.25), residues: 411
  loop : -1.71 (0.21), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 206 
 HIS   0.006   0.001   HIS A 533 
 PHE   0.018   0.001   PHE A 586 
 TYR   0.018   0.002   TYR D 184 
 ARG   0.004   0.000   ARG B 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04009 (  579)
  hydrogen bonds       : angle       4.83884 ( 1620)
  covalent geometry    : bond        0.00300 (13385)
  covalent geometry    : angle       0.54393 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 1.443 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A   76 CYS cc_start: 0.8047 (m) cc_final: 0.7776 (m)
REVERT: A  667 THR cc_start: 0.8504 (t) cc_final: 0.8278 (m)
REVERT: A  780 LEU cc_start: 0.8901 (mt) cc_final: 0.8248 (tt)
REVERT: A  804 PHE cc_start: 0.7889 (t80) cc_final: 0.7553 (t80)
REVERT: C   34 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7943 (mm-40)
REVERT: D  112 ARG cc_start: 0.8198 (ttt-90) cc_final: 0.7845 (ttt-90)
  outliers start: 2
  outliers final: 1
  residues processed: 188
  average time/residue: 0.2514
  time to fit residues: 69.2026
Evaluate side-chains
  149 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 143 optimal weight:    9.9990
   chunk 86 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 155 optimal weight:    0.4980
   chunk 18 optimal weight:    0.2980
   chunk 60 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
A 259 ASN
B 186 ASN
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  80 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.114339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.089430 restraints weight = 26484.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.087620 restraints weight = 26824.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.088644 restraints weight = 29767.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13385  Z= 0.099
  Angle     :  0.508   7.928  18175  Z= 0.272
  Chirality :  0.043   0.156   1995
  Planarity :  0.004   0.056   2399
  Dihedral  :  4.119  23.564   1839
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.75 %
    Favored  : 96.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.21), residues: 1662
  helix:  1.76 (0.25), residues: 429
  sheet: -0.35 (0.25), residues: 413
  loop : -1.61 (0.21), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 206 
 HIS   0.005   0.001   HIS A  30 
 PHE   0.017   0.001   PHE A 586 
 TYR   0.020   0.001   TYR D 184 
 ARG   0.004   0.000   ARG A  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  579)
  hydrogen bonds       : angle       4.51584 ( 1620)
  covalent geometry    : bond        0.00215 (13385)
  covalent geometry    : angle       0.50843 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 208
  time to evaluate  : 1.569 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A   76 CYS cc_start: 0.7860 (m) cc_final: 0.7618 (m)
REVERT: A  667 THR cc_start: 0.8475 (t) cc_final: 0.8211 (m)
REVERT: A  780 LEU cc_start: 0.8876 (mt) cc_final: 0.8267 (tt)
REVERT: A  804 PHE cc_start: 0.7815 (t80) cc_final: 0.7544 (t80)
REVERT: C   34 GLN cc_start: 0.8236 (mm-40) cc_final: 0.8017 (mm-40)
REVERT: D   52 ILE cc_start: 0.9158 (mt) cc_final: 0.8732 (mt)
REVERT: D  104 ASN cc_start: 0.8707 (m-40) cc_final: 0.8474 (m-40)
REVERT: D  146 ASP cc_start: 0.7974 (m-30) cc_final: 0.7435 (m-30)
REVERT: F   83 MET cc_start: 0.8623 (tpp) cc_final: 0.8422 (tpp)
REVERT: F   87 MET cc_start: 0.7926 (tpt) cc_final: 0.7438 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 210
  average time/residue: 0.2513
  time to fit residues: 77.9398
Evaluate side-chains
  154 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 144 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 95 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 122 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 533 HIS
A 561 GLN
B 170 GLN
B 264 ASN
B 347 HIS
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.112835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.086231 restraints weight = 26255.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.086312 restraints weight = 26455.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.087054 restraints weight = 23875.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13385  Z= 0.137
  Angle     :  0.530   8.066  18175  Z= 0.283
  Chirality :  0.043   0.148   1995
  Planarity :  0.004   0.057   2399
  Dihedral  :  4.186  24.326   1839
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.33 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.21), residues: 1662
  helix:  1.82 (0.25), residues: 428
  sheet: -0.33 (0.25), residues: 410
  loop : -1.64 (0.21), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 546 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.021   0.001   PHE A  24 
 TYR   0.018   0.001   TYR C  31 
 ARG   0.003   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03586 (  579)
  hydrogen bonds       : angle       4.48517 ( 1620)
  covalent geometry    : bond        0.00313 (13385)
  covalent geometry    : angle       0.53033 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 192
  time to evaluate  : 1.433 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A   76 CYS cc_start: 0.7944 (m) cc_final: 0.7687 (m)
REVERT: A  667 THR cc_start: 0.8451 (t) cc_final: 0.8122 (m)
REVERT: A  768 MET cc_start: 0.6873 (tmm) cc_final: 0.6653 (tmm)
REVERT: A  780 LEU cc_start: 0.8921 (mt) cc_final: 0.8271 (tt)
REVERT: A  804 PHE cc_start: 0.7943 (t80) cc_final: 0.7532 (t80)
REVERT: C   34 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7961 (mm-40)
REVERT: D  104 ASN cc_start: 0.8776 (m-40) cc_final: 0.8517 (m-40)
REVERT: D  146 ASP cc_start: 0.7972 (m-30) cc_final: 0.7496 (m-30)
REVERT: F   87 MET cc_start: 0.7946 (tpt) cc_final: 0.7414 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 194
  average time/residue: 0.2356
  time to fit residues: 68.3797
Evaluate side-chains
  150 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 99 optimal weight:    9.9990
   chunk 37 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 108 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 141 optimal weight:    6.9990
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
A 533 HIS
A 561 GLN
B 264 ASN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.109551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.084857 restraints weight = 26923.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.083453 restraints weight = 31093.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.083992 restraints weight = 34022.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  13385  Z= 0.246
  Angle     :  0.624   7.753  18175  Z= 0.333
  Chirality :  0.046   0.206   1995
  Planarity :  0.005   0.059   2399
  Dihedral  :  4.576  24.802   1839
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.54 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.21), residues: 1662
  helix:  1.38 (0.25), residues: 447
  sheet: -0.43 (0.26), residues: 393
  loop : -1.80 (0.21), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 546 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.032   0.002   PHE A 586 
 TYR   0.023   0.002   TYR E  37 
 ARG   0.005   0.000   ARG A  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04319 (  579)
  hydrogen bonds       : angle       4.75007 ( 1620)
  covalent geometry    : bond        0.00563 (13385)
  covalent geometry    : angle       0.62363 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 185
  time to evaluate  : 1.483 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A   30 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7268 (m90)
REVERT: A  667 THR cc_start: 0.8514 (t) cc_final: 0.8217 (m)
REVERT: A  780 LEU cc_start: 0.8886 (mt) cc_final: 0.8235 (tt)
REVERT: A  804 PHE cc_start: 0.8011 (t80) cc_final: 0.7660 (t80)
REVERT: C   34 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7915 (mm-40)
REVERT: D   52 ILE cc_start: 0.9262 (mt) cc_final: 0.8804 (mt)
REVERT: D  109 MET cc_start: 0.8787 (mtt) cc_final: 0.8535 (mtt)
REVERT: F   76 MET cc_start: 0.7826 (ttt) cc_final: 0.7366 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 188
  average time/residue: 0.2793
  time to fit residues: 77.2619
Evaluate side-chains
  146 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 115 optimal weight:    3.9990
   chunk 163 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 156 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 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 = 0.3409 r_free = 0.3409 target = 0.111264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.087076 restraints weight = 26811.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.085941 restraints weight = 30089.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.086772 restraints weight = 28220.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13385  Z= 0.159
  Angle     :  0.565   8.625  18175  Z= 0.303
  Chirality :  0.044   0.152   1995
  Planarity :  0.004   0.058   2399
  Dihedral  :  4.439  24.952   1839
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.76 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.21), residues: 1662
  helix:  1.50 (0.25), residues: 436
  sheet: -0.46 (0.26), residues: 402
  loop : -1.77 (0.21), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 546 
 HIS   0.005   0.001   HIS A 533 
 PHE   0.024   0.001   PHE A 586 
 TYR   0.021   0.002   TYR A 585 
 ARG   0.003   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  579)
  hydrogen bonds       : angle       4.62349 ( 1620)
  covalent geometry    : bond        0.00363 (13385)
  covalent geometry    : angle       0.56452 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A  667 THR cc_start: 0.8527 (t) cc_final: 0.8218 (m)
REVERT: A  780 LEU cc_start: 0.8866 (mt) cc_final: 0.8206 (tt)
REVERT: C   34 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7922 (mm-40)
REVERT: F   76 MET cc_start: 0.7758 (ttt) cc_final: 0.7292 (tmm)
REVERT: F   77 ASP cc_start: 0.7777 (m-30) cc_final: 0.7558 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 196
  average time/residue: 0.2462
  time to fit residues: 72.3278
Evaluate side-chains
  146 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 151 optimal weight:   10.0000
   chunk 106 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0010
   chunk 31 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 149 optimal weight:   10.0000
   overall best weight:    2.7792

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** 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 = 0.3405 r_free = 0.3405 target = 0.111152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.087041 restraints weight = 26868.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.085792 restraints weight = 30693.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.086549 restraints weight = 32395.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13385  Z= 0.178
  Angle     :  0.582   8.502  18175  Z= 0.310
  Chirality :  0.045   0.196   1995
  Planarity :  0.004   0.056   2399
  Dihedral  :  4.491  24.825   1839
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.13 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.21), residues: 1662
  helix:  1.36 (0.25), residues: 440
  sheet: -0.42 (0.26), residues: 397
  loop : -1.83 (0.21), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 546 
 HIS   0.005   0.001   HIS A 533 
 PHE   0.024   0.001   PHE A 586 
 TYR   0.022   0.002   TYR E  37 
 ARG   0.005   0.000   ARG B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04041 (  579)
  hydrogen bonds       : angle       4.65197 ( 1620)
  covalent geometry    : bond        0.00407 (13385)
  covalent geometry    : angle       0.58226 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 189
  time to evaluate  : 1.457 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A  768 MET cc_start: 0.6728 (tmm) cc_final: 0.6460 (tmm)
REVERT: A  780 LEU cc_start: 0.8893 (mt) cc_final: 0.8245 (tt)
REVERT: B   26 GLU cc_start: 0.6118 (tt0) cc_final: 0.5744 (mp0)
REVERT: D   52 ILE cc_start: 0.9263 (mt) cc_final: 0.8812 (mt)
REVERT: D  146 ASP cc_start: 0.8005 (m-30) cc_final: 0.7562 (m-30)
REVERT: F   76 MET cc_start: 0.7740 (ttt) cc_final: 0.7297 (tmm)
  outliers start: 2
  outliers final: 1
  residues processed: 191
  average time/residue: 0.2412
  time to fit residues: 67.9502
Evaluate side-chains
  146 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 118 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 125 optimal weight:    2.9990
   chunk 143 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** 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 = 0.3414 r_free = 0.3414 target = 0.111751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.086863 restraints weight = 26791.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.086482 restraints weight = 30313.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.086978 restraints weight = 30285.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13385  Z= 0.140
  Angle     :  0.559   8.943  18175  Z= 0.298
  Chirality :  0.044   0.175   1995
  Planarity :  0.004   0.055   2399
  Dihedral  :  4.406  24.910   1839
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.92 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.21), residues: 1662
  helix:  1.51 (0.25), residues: 434
  sheet: -0.38 (0.26), residues: 393
  loop : -1.72 (0.21), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F 413 
 HIS   0.005   0.001   HIS A 533 
 PHE   0.020   0.001   PHE A 586 
 TYR   0.020   0.001   TYR E  37 
 ARG   0.003   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  579)
  hydrogen bonds       : angle       4.55091 ( 1620)
  covalent geometry    : bond        0.00319 (13385)
  covalent geometry    : angle       0.55925 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 1.443 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A  768 MET cc_start: 0.6857 (tmm) cc_final: 0.6611 (tmm)
REVERT: A  780 LEU cc_start: 0.8919 (mt) cc_final: 0.8256 (tt)
REVERT: B  388 TYR cc_start: 0.7614 (m-80) cc_final: 0.7182 (m-80)
REVERT: F   76 MET cc_start: 0.7731 (ttt) cc_final: 0.7313 (tmm)
REVERT: F   77 ASP cc_start: 0.7849 (m-30) cc_final: 0.7642 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 185
  average time/residue: 0.2354
  time to fit residues: 64.6581
Evaluate side-chains
  146 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 143 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 144 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0020
   overall best weight:    1.1996

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 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 = 0.3436 r_free = 0.3436 target = 0.113347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.087656 restraints weight = 26600.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.087050 restraints weight = 26901.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.087761 restraints weight = 26263.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13385  Z= 0.113
  Angle     :  0.547   9.111  18175  Z= 0.289
  Chirality :  0.043   0.166   1995
  Planarity :  0.004   0.055   2399
  Dihedral  :  4.274  25.162   1839
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.57 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.21), residues: 1662
  helix:  1.62 (0.25), residues: 431
  sheet: -0.48 (0.25), residues: 417
  loop : -1.59 (0.22), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP F 413 
 HIS   0.004   0.001   HIS A 533 
 PHE   0.018   0.001   PHE A 586 
 TYR   0.019   0.001   TYR D 184 
 ARG   0.002   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03491 (  579)
  hydrogen bonds       : angle       4.45364 ( 1620)
  covalent geometry    : bond        0.00255 (13385)
  covalent geometry    : angle       0.54659 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 190
  time to evaluate  : 1.518 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A   76 CYS cc_start: 0.7897 (m) cc_final: 0.7612 (m)
REVERT: A  780 LEU cc_start: 0.8944 (mt) cc_final: 0.8276 (tt)
REVERT: C   43 GLU cc_start: 0.7728 (pm20) cc_final: 0.7309 (tt0)
REVERT: D   52 ILE cc_start: 0.9166 (mt) cc_final: 0.8734 (mt)
REVERT: F   76 MET cc_start: 0.7768 (ttt) cc_final: 0.7302 (tmm)
  outliers start: 2
  outliers final: 1
  residues processed: 192
  average time/residue: 0.2361
  time to fit residues: 68.2862
Evaluate side-chains
  153 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 1.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 150 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 99 optimal weight:    9.9990
   chunk 135 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** 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 = 0.3402 r_free = 0.3402 target = 0.110872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.085929 restraints weight = 26670.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.085342 restraints weight = 28789.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.086013 restraints weight = 30043.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13385  Z= 0.178
  Angle     :  0.599   8.981  18175  Z= 0.316
  Chirality :  0.045   0.181   1995
  Planarity :  0.004   0.055   2399
  Dihedral  :  4.477  25.121   1839
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.35 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.21), residues: 1662
  helix:  1.48 (0.25), residues: 431
  sheet: -0.50 (0.25), residues: 416
  loop : -1.67 (0.21), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 206 
 HIS   0.005   0.001   HIS A 533 
 PHE   0.024   0.001   PHE A 586 
 TYR   0.022   0.002   TYR A 230 
 ARG   0.003   0.000   ARG D 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  579)
  hydrogen bonds       : angle       4.58701 ( 1620)
  covalent geometry    : bond        0.00409 (13385)
  covalent geometry    : angle       0.59911 (18175)

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it.
REVERT: A   30 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7431 (m90)
REVERT: A   76 CYS cc_start: 0.7835 (m) cc_final: 0.7615 (m)
REVERT: A  780 LEU cc_start: 0.8939 (mt) cc_final: 0.8256 (tt)
REVERT: C   43 GLU cc_start: 0.7759 (pm20) cc_final: 0.7317 (tt0)
REVERT: F   76 MET cc_start: 0.7843 (ttt) cc_final: 0.7314 (tmm)
  outliers start: 2
  outliers final: 1
  residues processed: 180
  average time/residue: 0.2367
  time to fit residues: 64.3540
Evaluate side-chains
  145 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 107 optimal weight:    9.9990
   chunk 124 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 154 optimal weight:    2.9990
   chunk 150 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 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 = 0.3412 r_free = 0.3412 target = 0.111651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.086582 restraints weight = 26855.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.084978 restraints weight = 31108.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.085801 restraints weight = 33194.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13385  Z= 0.156
  Angle     :  0.579   9.173  18175  Z= 0.307
  Chirality :  0.044   0.173   1995
  Planarity :  0.004   0.055   2399
  Dihedral  :  4.443  24.989   1839
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.21 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.21), residues: 1662
  helix:  1.46 (0.25), residues: 431
  sheet: -0.51 (0.25), residues: 416
  loop : -1.64 (0.22), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP F 413 
 HIS   0.005   0.001   HIS A 533 
 PHE   0.022   0.001   PHE A 586 
 TYR   0.023   0.002   TYR A 230 
 ARG   0.003   0.000   ARG D 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03822 (  579)
  hydrogen bonds       : angle       4.60353 ( 1620)
  covalent geometry    : bond        0.00356 (13385)
  covalent geometry    : angle       0.57888 (18175)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3652.31 seconds
wall clock time: 64 minutes 23.11 seconds (3863.11 seconds total)