Starting phenix.real_space_refine
on Thu Feb 13 14:40:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nd1_0440/02_2025/6nd1_0440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nd1_0440/02_2025/6nd1_0440.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nd1_0440/02_2025/6nd1_0440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nd1_0440/02_2025/6nd1_0440.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nd1_0440/02_2025/6nd1_0440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nd1_0440/02_2025/6nd1_0440.cif"
  }
  resolution = 4.1
  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=   0.008
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      36      5.16       5
     C    5990      2.51       5
     N    1514      2.21       5
     O    1646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9186
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3031
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 17, 'TRANS': 372}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 3565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3565
          Classifications: {'peptide': 461}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 27, 'TRANS': 433}
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 179
          Unresolved non-hydrogen angles: 236
          Unresolved non-hydrogen dihedrals: 152
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 95
    Chain: "C"
      Number of atoms: 443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 443
          Classifications: {'peptide': 56}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 53}
    Chain: "D"
      Number of atoms: 270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 270
          Classifications: {'peptide': 41}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 39}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "E"
      Number of atoms: 1143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1143
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 4, 'TRANS': 134}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 734
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU A 284 " occ=0.88
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 284 " occ=0.75
    residue:
      pdb=" N   GLY A 316 " occ=0.88
      ... (2 atoms not shown)
      pdb=" O   GLY A 316 " occ=0.88
    residue:
      pdb=" N   LEU A 398 " occ=0.88
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 398 " occ=0.75
    residue:
      pdb=" N   ALA A 413 " occ=0.88
      ... (3 atoms not shown)
      pdb=" CB  ALA A 413 " occ=0.88
  Time building chain proxies: 5.34, per 1000 atoms: 0.58
  Number of scatterers: 9186
  At special positions: 0
  Unit cell: (108, 106.65, 121.5, 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      36     16.00
     O    1646      8.00
     N    1514      7.00
     C    5990      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: 2.32
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2228

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      65.8% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 48
      removed outlier: 3.743A  pdb=" N   ILE B  34 " --> pdb=" O   ASN B  30 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   THR B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LEU B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ILE B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 71
      removed outlier: 4.073A  pdb=" N   MET B  69 " --> pdb=" O   TRP B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.731A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER B  88 " --> pdb=" O   PRO B  84 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER B  89 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   PHE B  92 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 137
    Processing helix  chain 'B' and resid 146 through 174
      removed outlier: 4.015A  pdb=" N   CYS B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLY B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 197
      removed outlier: 3.878A  pdb=" N   LEU B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE B 184 " --> pdb=" O   GLY B 180 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ILE B 189 " --> pdb=" O   THR B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 223
      removed outlier: 3.998A  pdb=" N   LEU B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU B 222 " --> pdb=" O   PHE B 218 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA B 223 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 238
      removed outlier: 4.208A  pdb=" N   VAL B 233 " --> pdb=" O   LYS B 229 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ARG B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 262
      removed outlier: 4.016A  pdb=" N   ALA B 252 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU B 258 " --> pdb=" O   PHE B 254 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLY B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 289
      removed outlier: 3.722A  pdb=" N   SER B 289 " --> pdb=" O   PHE B 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 286 through 289'
    Processing helix  chain 'B' and resid 290 through 314
      removed outlier: 3.707A  pdb=" N   MET B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B 295 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE B 304 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU B 305 " --> pdb=" O   SER B 301 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ILE B 306 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER B 307 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 384
      removed outlier: 4.000A  pdb=" N   THR B 362 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE B 363 " --> pdb=" O   PRO B 359 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLU B 382 " --> pdb=" O   LYS B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 399
      removed outlier: 4.170A  pdb=" N   LYS B 393 " --> pdb=" O   ARG B 389 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN B 398 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 440
      removed outlier: 3.870A  pdb=" N   LYS B 416 " --> pdb=" O   ARG B 412 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE B 417 " --> pdb=" O   GLU B 413 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
      removed outlier: 3.628A  pdb=" N   ASP B 437 " --> pdb=" O   SER B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 464
      removed outlier: 3.595A  pdb=" N   ILE B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR B 454 " --> pdb=" O   MET B 450 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LYS B 464 " --> pdb=" O   GLU B 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 15 through 21
      removed outlier: 4.027A  pdb=" N   THR A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY A  21 " --> pdb=" O   PHE A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 36
    Processing helix  chain 'A' and resid 59 through 64
      removed outlier: 4.385A  pdb=" N   GLU A  64 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 78
      removed outlier: 3.590A  pdb=" N   PHE A  78 " --> pdb=" O   PHE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 110
    Processing helix  chain 'A' and resid 221 through 232
      removed outlier: 3.541A  pdb=" N   VAL A 225 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   TYR A 227 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 246
      removed outlier: 3.678A  pdb=" N   VAL A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER A 240 " --> pdb=" O   PRO A 236 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.861A  pdb=" N   ASN A 268 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 286
      removed outlier: 3.828A  pdb=" N   ILE A 280 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 311
      removed outlier: 3.794A  pdb=" N   GLU A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   LYS A 304 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A 305 " --> pdb=" O   ASP A 301 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   HIS A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 328
    Processing helix  chain 'A' and resid 328 through 341
      removed outlier: 3.893A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 360
      removed outlier: 3.855A  pdb=" N   PHE A 356 " --> pdb=" O   ALA A 352 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 4.100A  pdb=" N   LEU A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN A 373 " --> pdb=" O   CYS A 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 368 through 373'
    Processing helix  chain 'A' and resid 378 through 386
    Processing helix  chain 'A' and resid 391 through 397
      removed outlier: 3.616A  pdb=" N   LEU A 395 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 407
    Processing helix  chain 'A' and resid 411 through 424
    Processing helix  chain 'A' and resid 480 through 484
    Processing helix  chain 'A' and resid 486 through 494
      removed outlier: 3.986A  pdb=" N   ALA A 489 " --> pdb=" O   ASP A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 3.523A  pdb=" N   TYR C  47 " --> pdb=" O   ASP C  43 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   THR C  48 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LYS C  52 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA C  53 " --> pdb=" O   LYS C  49 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS C  69 " --> pdb=" O   GLY C  65 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
      removed outlier: 3.682A  pdb=" N   TYR C  77 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 47
      removed outlier: 3.767A  pdb=" N   ALA D  47 " --> pdb=" O   TYR D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 75
      removed outlier: 3.818A  pdb=" N   PHE D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL D  73 " --> pdb=" O   VAL D  69 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE D  74 " --> pdb=" O   ALA D  70 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 60
      removed outlier: 4.378A  pdb=" N   LEU E  34 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE E  59 " --> pdb=" O   GLN E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 70 through 81
      removed outlier: 4.198A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   GLN E  77 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE E  78 " --> pdb=" O   LEU E  74 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   MET E  81 " --> pdb=" O   GLN E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 124
      Proline residue:  E 115  - end of helix
      removed outlier: 3.862A  pdb=" N   GLY E 124 " --> pdb=" O   LEU E 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 127 through 153
      removed outlier: 3.680A  pdb=" N   TRP E 131 " --> pdb=" O   GLY E 127 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU E 149 " --> pdb=" O   PHE E 145 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 159 through 176
      removed outlier: 4.282A  pdb=" N   VAL E 164 " --> pdb=" O   VAL E 160 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   MET E 165 " --> pdb=" O   GLN E 161 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   VAL E 166 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   CYS E 167 " --> pdb=" O   PHE E 163 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   LYS E 168 " --> pdb=" O   VAL E 164 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLU E 169 " --> pdb=" O   MET E 165 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN E 174 " --> pdb=" O   ILE E 170 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 120
    Processing helix  chain 'F' and resid 122 through 136
      removed outlier: 3.792A  pdb=" N   LEU F 126 " --> pdb=" O   HIS F 122 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLN F 127 " --> pdb=" O   LEU F 123 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ASP F 128 " --> pdb=" O   GLU F 124 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE F 131 " --> pdb=" O   GLN F 127 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY F 136 " --> pdb=" O   LEU F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 139 through 152
      removed outlier: 4.120A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL F 144 " --> pdb=" O   PRO F 140 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 170
    Processing helix  chain 'F' and resid 175 through 192
      removed outlier: 3.629A  pdb=" N   LEU F 179 " --> pdb=" O   LYS F 175 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 203
      removed outlier: 5.832A  pdb=" N   THR B 201 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU B 212 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLU B 210 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 269
    Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 436
      removed outlier: 3.969A  pdb=" N   LYS A 432 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 525
      removed outlier: 3.575A  pdb=" N   LYS A 524 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 524 through 525
      removed outlier: 3.575A  pdb=" N   LYS A 524 " --> pdb=" O   SER A 519 " (cutoff:3.500A)

    506 hydrogen bonds defined for protein.
    1473 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 2.69 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: 2687
        1.34 -     1.46: 1685
        1.46 -     1.58: 4938
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 9366
  Sorted by residual:
  bond pdb=" C   THR B 379 "
       pdb=" N   TRP B 380 "
    ideal  model  delta    sigma   weight residual
    1.335  1.226  0.110 1.38e-02 5.25e+03 6.30e+01
  bond pdb=" C   TRP A 566 "
       pdb=" N   GLU A 567 "
    ideal  model  delta    sigma   weight residual
    1.331  1.238  0.093 1.37e-02 5.33e+03 4.61e+01
  bond pdb=" C   GLY A 576 "
       pdb=" N   GLN A 577 "
    ideal  model  delta    sigma   weight residual
    1.331  1.221  0.110 2.07e-02 2.33e+03 2.83e+01
  bond pdb=" C   GLN B 398 "
       pdb=" N   GLY B 399 "
    ideal  model  delta    sigma   weight residual
    1.330  1.258  0.072 1.42e-02 4.96e+03 2.56e+01
  bond pdb=" N   ILE C  79 "
       pdb=" CA  ILE C  79 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.10e+00
  ... (remaining 9361 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.03: 12522
        4.03 -     8.06: 127
        8.06 -    12.09: 30
       12.09 -    16.11: 3
       16.11 -    20.14: 3
  Bond angle restraints: 12685
  Sorted by residual:
  angle pdb=" C   ILE C  75 "
        pdb=" CA  ILE C  75 "
        pdb=" CB  ILE C  75 "
      ideal   model   delta    sigma   weight residual
     112.14  129.12  -16.98 1.35e+00 5.49e-01 1.58e+02
  angle pdb=" C   GLU F 124 "
        pdb=" CA  GLU F 124 "
        pdb=" CB  GLU F 124 "
      ideal   model   delta    sigma   weight residual
     110.85  130.99  -20.14 1.70e+00 3.46e-01 1.40e+02
  angle pdb=" C   ALA B 463 "
        pdb=" CA  ALA B 463 "
        pdb=" CB  ALA B 463 "
      ideal   model   delta    sigma   weight residual
     110.68  125.60  -14.92 1.70e+00 3.46e-01 7.70e+01
  angle pdb=" C   GLU A 440 "
        pdb=" CA  GLU A 440 "
        pdb=" CB  GLU A 440 "
      ideal   model   delta    sigma   weight residual
     110.45   91.69   18.76 2.15e+00 2.16e-01 7.61e+01
  angle pdb=" C   PHE B 218 "
        pdb=" CA  PHE B 218 "
        pdb=" CB  PHE B 218 "
      ideal   model   delta    sigma   weight residual
     109.56  123.30  -13.74 1.65e+00 3.67e-01 6.94e+01
  ... (remaining 12680 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 4902
       17.48 -    34.95: 569
       34.95 -    52.43: 124
       52.43 -    69.91: 28
       69.91 -    87.39: 14
  Dihedral angle restraints: 5637
    sinusoidal: 2211
      harmonic: 3426
  Sorted by residual:
  dihedral pdb=" C   GLU A 440 "
           pdb=" N   GLU A 440 "
           pdb=" CA  GLU A 440 "
           pdb=" CB  GLU A 440 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -100.10  -22.50     0      2.50e+00 1.60e-01 8.10e+01
  dihedral pdb=" C   GLU F 124 "
           pdb=" N   GLU F 124 "
           pdb=" CA  GLU F 124 "
           pdb=" CB  GLU F 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -143.24   20.64     0      2.50e+00 1.60e-01 6.82e+01
  dihedral pdb=" CA  PRO B  62 "
           pdb=" C   PRO B  62 "
           pdb=" N   LEU B  63 "
           pdb=" CA  LEU B  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.65   39.35     0      5.00e+00 4.00e-02 6.19e+01
  ... (remaining 5634 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1385
       0.131 -    0.261: 89
       0.261 -    0.392: 11
       0.392 -    0.523: 6
       0.523 -    0.654: 2
  Chirality restraints: 1493
  Sorted by residual:
  chirality pdb=" CA  GLU F 124 "
            pdb=" N   GLU F 124 "
            pdb=" C   GLU F 124 "
            pdb=" CB  GLU F 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" CA  PHE B 236 "
            pdb=" N   PHE B 236 "
            pdb=" C   PHE B 236 "
            pdb=" CB  PHE B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.20e+00
  chirality pdb=" CA  ALA B 462 "
            pdb=" N   ALA B 462 "
            pdb=" C   ALA B 462 "
            pdb=" CB  ALA B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.96    0.52 2.00e-01 2.50e+01 6.80e+00
  ... (remaining 1490 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 444 "   -0.059 5.00e-02 4.00e+02   9.00e-02 1.30e+01
        pdb=" N   PRO A 445 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO A 445 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 445 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 265 "   -0.015 2.00e-02 2.50e+03   3.07e-02 9.43e+00
        pdb=" C   TYR B 265 "    0.053 2.00e-02 2.50e+03
        pdb=" O   TYR B 265 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU B 266 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 160 "   -0.015 2.00e-02 2.50e+03   3.06e-02 9.38e+00
        pdb=" C   VAL E 160 "    0.053 2.00e-02 2.50e+03
        pdb=" O   VAL E 160 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLN E 161 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2168
        2.78 -     3.31: 8588
        3.31 -     3.84: 14120
        3.84 -     4.37: 15051
        4.37 -     4.90: 26046
  Nonbonded interactions: 65973
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 599 "
            pdb=" N   THR A 600 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG1 THR A 444 "
            pdb=" OG  SER A 447 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   HIS A 390 "
            pdb=" OH  TYR F 190 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   SER A 483 "
            pdb=" OG  SER A 483 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ASN B 290 "
            pdb=" OD1 ASN B 290 "
     model   vdw
     2.302 3.040
  ... (remaining 65968 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=0.75 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  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:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.440
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.110   9366  Z= 0.580
  Angle     :  1.231  20.144  12685  Z= 0.718
  Chirality :  0.079   0.654   1493
  Planarity :  0.009   0.090   1586
  Dihedral  : 16.242  87.386   3409
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.67 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 15.61 %
    Favored  : 84.29 %
  Cbeta Deviations :  1.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.89 (0.20), residues: 1145
  helix: -2.28 (0.15), residues: 689
  sheet: -2.93 (0.45), residues: 80
  loop : -2.70 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 242 
 HIS   0.011   0.002   HIS A 334 
 PHE   0.041   0.003   PHE E  66 
 TYR   0.030   0.002   TYR B 287 
 ARG   0.009   0.001   ARG A 509 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 251
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  119 LYS cc_start: 0.5483 (tttt) cc_final: 0.4969 (tttt)
REVERT: B  237 TYR cc_start: 0.7040 (m-80) cc_final: 0.6619 (m-80)
REVERT: B  238 ARG cc_start: 0.7011 (mmm160) cc_final: 0.5533 (mmm160)
REVERT: B  400 MET cc_start: 0.8025 (mtt) cc_final: 0.7735 (mtm)
REVERT: B  406 ARG cc_start: 0.7122 (mpt-90) cc_final: 0.6734 (mpt-90)
REVERT: A  359 ILE cc_start: 0.9160 (mm) cc_final: 0.8940 (mp)
REVERT: A  431 ILE cc_start: 0.8864 (mt) cc_final: 0.8610 (mm)
REVERT: A  473 GLU cc_start: 0.7963 (tp30) cc_final: 0.7537 (tp30)
REVERT: A  491 MET cc_start: 0.8933 (mtp) cc_final: 0.8639 (mtp)
REVERT: A  521 LYS cc_start: 0.9150 (tptm) cc_final: 0.8519 (ttmt)
REVERT: A  562 ASP cc_start: 0.6913 (p0) cc_final: 0.6705 (p0)
REVERT: C   49 LYS cc_start: 0.8446 (tttp) cc_final: 0.8129 (tttt)
REVERT: E   46 MET cc_start: 0.6966 (ttm) cc_final: 0.6523 (tmm)
REVERT: E   54 LYS cc_start: 0.7560 (tttt) cc_final: 0.7030 (tmtt)
REVERT: E   99 ARG cc_start: 0.6868 (ttp-170) cc_final: 0.6605 (mmm-85)
REVERT: E  165 MET cc_start: 0.6274 (mmm) cc_final: 0.6073 (mmp)
REVERT: F  152 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8334 (mmmt)
REVERT: F  158 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7866 (mt-10)
REVERT: F  182 GLU cc_start: 0.7656 (tp30) cc_final: 0.7260 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 252
  average time/residue: 0.2403
  time to fit residues: 81.1454
Evaluate side-chains
  192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:   20.0000
   chunk 90 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0030
   chunk 105 optimal weight:   10.0000
   overall best weight:    0.9192

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

Flipped N/Q/H residues before XYZ refinement:
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 ASN
B 220 HIS
B 261 GLN
B 347 GLN
B 403 ASN
A  55 ASN
A 255 HIS
A 261 ASN
A 334 HIS
A 376 ASN
A 427 ASN
A 494 GLN
F 106 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.145984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.115088 restraints weight = 17162.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.117015 restraints weight = 12040.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.118127 restraints weight = 9594.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3319
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9366  Z= 0.184
  Angle     :  0.638   9.115  12685  Z= 0.324
  Chirality :  0.043   0.154   1493
  Planarity :  0.005   0.066   1586
  Dihedral  :  5.409  71.694   1242
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.88 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.82 (0.23), residues: 1145
  helix: -0.49 (0.18), residues: 720
  sheet: -2.27 (0.50), residues: 77
  loop : -2.25 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  65 
 HIS   0.007   0.001   HIS A 255 
 PHE   0.023   0.001   PHE E  66 
 TYR   0.016   0.001   TYR B 344 
 ARG   0.004   0.000   ARG E 105 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 252
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  119 LYS cc_start: 0.5335 (tttt) cc_final: 0.4903 (tttt)
REVERT: B  131 LEU cc_start: 0.8778 (tp) cc_final: 0.8532 (tp)
REVERT: B  261 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8273 (mm-40)
REVERT: B  400 MET cc_start: 0.7843 (mtt) cc_final: 0.7557 (mtm)
REVERT: B  406 ARG cc_start: 0.7179 (mpt-90) cc_final: 0.6709 (mpt-90)
REVERT: B  439 LEU cc_start: 0.9278 (tt) cc_final: 0.8667 (mt)
REVERT: A  336 LEU cc_start: 0.8891 (tp) cc_final: 0.8439 (tt)
REVERT: A  376 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8243 (m110)
REVERT: A  431 ILE cc_start: 0.8775 (mt) cc_final: 0.8481 (mm)
REVERT: A  521 LYS cc_start: 0.9042 (tptm) cc_final: 0.8329 (ttmt)
REVERT: A  562 ASP cc_start: 0.6319 (p0) cc_final: 0.5824 (p0)
REVERT: A  601 ASP cc_start: 0.7921 (m-30) cc_final: 0.7643 (m-30)
REVERT: E   46 MET cc_start: 0.6932 (ttm) cc_final: 0.6473 (tmm)
REVERT: E   54 LYS cc_start: 0.7738 (tttt) cc_final: 0.7237 (tmtt)
REVERT: E   99 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6368 (mmm-85)
REVERT: E  103 SER cc_start: 0.8815 (p) cc_final: 0.8460 (p)
REVERT: E  165 MET cc_start: 0.6346 (mmm) cc_final: 0.5521 (mpp)
REVERT: F  110 ARG cc_start: 0.6407 (tmm-80) cc_final: 0.6193 (tmm-80)
REVERT: F  152 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8294 (mmmt)
REVERT: F  182 GLU cc_start: 0.7731 (tp30) cc_final: 0.7351 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 255
  average time/residue: 0.2140
  time to fit residues: 75.4200
Evaluate side-chains
  199 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 196
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 2 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0570
   chunk 112 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.3102

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 ASN
A 307 GLN
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 GLN
E  69 ASN
E  72 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.146387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.115313 restraints weight = 17543.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117464 restraints weight = 11863.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.118695 restraints weight = 9205.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9366  Z= 0.188
  Angle     :  0.596   7.837  12685  Z= 0.301
  Chirality :  0.042   0.182   1493
  Planarity :  0.004   0.058   1586
  Dihedral  :  4.863  60.784   1242
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.00 %
    Favored  : 94.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.24), residues: 1145
  helix:  0.22 (0.19), residues: 722
  sheet: -1.83 (0.54), residues: 77
  loop : -2.02 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  65 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.018   0.001   PHE E  66 
 TYR   0.017   0.001   TYR B 344 
 ARG   0.004   0.000   ARG E 106 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  238 ARG cc_start: 0.6722 (mmm160) cc_final: 0.5351 (mmm160)
REVERT: B  249 MET cc_start: 0.8322 (mmm) cc_final: 0.7619 (mmm)
REVERT: B  347 GLN cc_start: 0.7219 (tm-30) cc_final: 0.7003 (tm-30)
REVERT: B  400 MET cc_start: 0.7871 (mtt) cc_final: 0.7557 (mtm)
REVERT: B  406 ARG cc_start: 0.7295 (mpt-90) cc_final: 0.6729 (mpt-90)
REVERT: B  439 LEU cc_start: 0.9273 (tt) cc_final: 0.8005 (tt)
REVERT: A  248 SER cc_start: 0.9206 (p) cc_final: 0.8979 (t)
REVERT: A  431 ILE cc_start: 0.8754 (mt) cc_final: 0.8439 (mm)
REVERT: A  521 LYS cc_start: 0.8943 (tptm) cc_final: 0.8275 (ttmt)
REVERT: A  562 ASP cc_start: 0.6241 (p0) cc_final: 0.5926 (p0)
REVERT: A  601 ASP cc_start: 0.7949 (m-30) cc_final: 0.7691 (m-30)
REVERT: E   46 MET cc_start: 0.7060 (ttm) cc_final: 0.6437 (tmm)
REVERT: E   54 LYS cc_start: 0.7914 (tttt) cc_final: 0.7319 (tmtt)
REVERT: E   99 ARG cc_start: 0.6705 (ttp-170) cc_final: 0.6383 (mmm-85)
REVERT: E  165 MET cc_start: 0.6253 (mmm) cc_final: 0.5434 (mpp)
REVERT: F  152 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8339 (mmmt)
REVERT: F  154 ARG cc_start: 0.7317 (mtp180) cc_final: 0.6201 (ttp80)
REVERT: F  158 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8418 (mt-10)
REVERT: F  182 GLU cc_start: 0.7767 (tp30) cc_final: 0.7335 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2203
  time to fit residues: 76.2172
Evaluate side-chains
  193 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 24 optimal weight:    0.4980
   chunk 35 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0870
   chunk 30 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   chunk 105 optimal weight:    6.9990
   chunk 74 optimal weight:    0.5980
   chunk 115 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 112 optimal weight:    7.9990
   overall best weight:    2.4362

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 330 HIS
A 427 ASN
E  69 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.143653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.112566 restraints weight = 17063.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.114491 restraints weight = 11491.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.115941 restraints weight = 8951.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9366  Z= 0.244
  Angle     :  0.626  10.388  12685  Z= 0.316
  Chirality :  0.044   0.200   1493
  Planarity :  0.004   0.061   1586
  Dihedral  :  4.768  56.773   1242
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.27 %
    Favored  : 96.63 %
  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: -0.68 (0.25), residues: 1145
  helix:  0.45 (0.19), residues: 730
  sheet: -1.61 (0.56), residues: 77
  loop : -2.07 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  35 
 HIS   0.003   0.001   HIS D  72 
 PHE   0.020   0.001   PHE E  66 
 TYR   0.023   0.001   TYR B 287 
 ARG   0.004   0.000   ARG E 106 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6377 (p0) cc_final: 0.6049 (p0)
REVERT: B  131 LEU cc_start: 0.9026 (tp) cc_final: 0.8793 (tp)
REVERT: B  236 PHE cc_start: 0.7082 (m-80) cc_final: 0.6545 (m-10)
REVERT: B  238 ARG cc_start: 0.6732 (mmm160) cc_final: 0.5496 (mmm160)
REVERT: B  347 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: B  400 MET cc_start: 0.7864 (mtt) cc_final: 0.7574 (mtm)
REVERT: B  406 ARG cc_start: 0.7164 (mpt-90) cc_final: 0.6715 (mpt-90)
REVERT: A  248 SER cc_start: 0.9217 (p) cc_final: 0.8962 (t)
REVERT: A  431 ILE cc_start: 0.8850 (mt) cc_final: 0.8518 (mm)
REVERT: A  521 LYS cc_start: 0.8983 (tptm) cc_final: 0.8369 (ttmt)
REVERT: A  562 ASP cc_start: 0.6450 (p0) cc_final: 0.6228 (p0)
REVERT: A  601 ASP cc_start: 0.8066 (m-30) cc_final: 0.7800 (m-30)
REVERT: A  606 MET cc_start: 0.9000 (mtm) cc_final: 0.8613 (mtp)
REVERT: E   46 MET cc_start: 0.7017 (ttm) cc_final: 0.6465 (tmm)
REVERT: E   54 LYS cc_start: 0.7942 (tttt) cc_final: 0.7362 (tmtt)
REVERT: E   97 LEU cc_start: 0.7906 (mt) cc_final: 0.7617 (mt)
REVERT: E  159 TRP cc_start: 0.7058 (t-100) cc_final: 0.6787 (t-100)
REVERT: E  165 MET cc_start: 0.6217 (mmm) cc_final: 0.5368 (mpp)
REVERT: F  150 LEU cc_start: 0.9072 (tt) cc_final: 0.8828 (tt)
REVERT: F  152 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8322 (mmmt)
REVERT: F  154 ARG cc_start: 0.7235 (mtp180) cc_final: 0.6204 (ttp80)
REVERT: F  158 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: F  182 GLU cc_start: 0.7689 (tp30) cc_final: 0.7479 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 228
  average time/residue: 0.2130
  time to fit residues: 66.9558
Evaluate side-chains
  195 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 71 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 42 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 ASN
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  69 ASN
E 123 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.141125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.110382 restraints weight = 16687.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.112237 restraints weight = 11350.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.113690 restraints weight = 8901.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9366  Z= 0.225
  Angle     :  0.618  10.516  12685  Z= 0.311
  Chirality :  0.044   0.182   1493
  Planarity :  0.004   0.061   1586
  Dihedral  :  4.648  54.761   1242
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.65 %
    Favored  : 97.14 %
  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: -0.39 (0.25), residues: 1145
  helix:  0.61 (0.19), residues: 728
  sheet: -1.51 (0.57), residues: 77
  loop : -1.75 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  35 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.014   0.001   PHE A 238 
 TYR   0.016   0.001   TYR B 344 
 ARG   0.003   0.000   ARG E  99 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 227
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6152 (p0) cc_final: 0.5882 (p0)
REVERT: B  129 GLN cc_start: 0.8385 (mp10) cc_final: 0.8116 (mp10)
REVERT: B  238 ARG cc_start: 0.6747 (mmm160) cc_final: 0.5450 (mmm160)
REVERT: B  249 MET cc_start: 0.8471 (mmm) cc_final: 0.7735 (mmm)
REVERT: B  347 GLN cc_start: 0.7269 (tm-30) cc_final: 0.7045 (tm-30)
REVERT: B  400 MET cc_start: 0.7919 (mtt) cc_final: 0.7624 (mtm)
REVERT: B  406 ARG cc_start: 0.7306 (mpt-90) cc_final: 0.6743 (mpt-90)
REVERT: A  248 SER cc_start: 0.9208 (p) cc_final: 0.8998 (t)
REVERT: A  402 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8440 (mmmt)
REVERT: A  431 ILE cc_start: 0.8961 (mt) cc_final: 0.8628 (mm)
REVERT: A  521 LYS cc_start: 0.8987 (tptm) cc_final: 0.8405 (ttmt)
REVERT: A  562 ASP cc_start: 0.6582 (p0) cc_final: 0.6368 (p0)
REVERT: A  601 ASP cc_start: 0.8075 (m-30) cc_final: 0.7792 (m-30)
REVERT: A  606 MET cc_start: 0.9025 (mtm) cc_final: 0.8712 (mtp)
REVERT: E   46 MET cc_start: 0.7033 (ttm) cc_final: 0.6404 (tmm)
REVERT: E   54 LYS cc_start: 0.7945 (tttt) cc_final: 0.7400 (tmtt)
REVERT: E  165 MET cc_start: 0.6057 (mmm) cc_final: 0.5322 (mpp)
REVERT: F  154 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6332 (ttp80)
REVERT: F  158 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7912 (mt-10)
REVERT: F  182 GLU cc_start: 0.7783 (tp30) cc_final: 0.7447 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2147
  time to fit residues: 67.4094
Evaluate side-chains
  193 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 91 optimal weight:    8.9990
   chunk 102 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
B 246 GLN
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 HIS
E  69 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.143812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.112650 restraints weight = 16792.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.114736 restraints weight = 11468.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.116049 restraints weight = 8931.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9366  Z= 0.169
  Angle     :  0.582  10.542  12685  Z= 0.289
  Chirality :  0.042   0.180   1493
  Planarity :  0.004   0.060   1586
  Dihedral  :  4.446  54.674   1242
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.84 %
    Favored  : 98.06 %
  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:  0.16 (0.26), residues: 1145
  helix:  1.02 (0.19), residues: 711
  sheet: -1.33 (0.59), residues: 75
  loop : -1.34 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 159 
 HIS   0.004   0.001   HIS D  72 
 PHE   0.013   0.001   PHE E  66 
 TYR   0.012   0.001   TYR B 344 
 ARG   0.003   0.000   ARG B 412 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 240
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
REVERT: B  238 ARG cc_start: 0.6660 (mmm160) cc_final: 0.5510 (mmm160)
REVERT: B  249 MET cc_start: 0.8411 (mmm) cc_final: 0.7769 (mmm)
REVERT: B  347 GLN cc_start: 0.7287 (tm-30) cc_final: 0.7012 (tm-30)
REVERT: B  377 SER cc_start: 0.8543 (m) cc_final: 0.8227 (t)
REVERT: B  400 MET cc_start: 0.7939 (mtt) cc_final: 0.7639 (mtm)
REVERT: B  406 ARG cc_start: 0.7221 (mpt-90) cc_final: 0.6683 (mpt-90)
REVERT: A  248 SER cc_start: 0.9152 (p) cc_final: 0.8934 (t)
REVERT: A  336 LEU cc_start: 0.8770 (tp) cc_final: 0.8443 (tt)
REVERT: A  521 LYS cc_start: 0.8863 (tptm) cc_final: 0.8257 (ttpt)
REVERT: A  562 ASP cc_start: 0.6580 (p0) cc_final: 0.6319 (p0)
REVERT: A  601 ASP cc_start: 0.7709 (m-30) cc_final: 0.7401 (m-30)
REVERT: E   46 MET cc_start: 0.7111 (ttm) cc_final: 0.6310 (tmm)
REVERT: E   54 LYS cc_start: 0.7944 (tttt) cc_final: 0.7407 (tmtt)
REVERT: E  165 MET cc_start: 0.5707 (mmm) cc_final: 0.5145 (mpp)
REVERT: F  154 ARG cc_start: 0.7378 (mtp180) cc_final: 0.6353 (ttp80)
REVERT: F  158 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8363 (mt-10)
REVERT: F  182 GLU cc_start: 0.7831 (tp30) cc_final: 0.7473 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 241
  average time/residue: 0.2082
  time to fit residues: 69.4546
Evaluate side-chains
  196 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 45 optimal weight:   30.0000
   chunk 90 optimal weight:   20.0000
   chunk 74 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.139650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.107903 restraints weight = 17132.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.109998 restraints weight = 11630.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.111218 restraints weight = 9021.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9366  Z= 0.239
  Angle     :  0.638  10.912  12685  Z= 0.320
  Chirality :  0.044   0.192   1493
  Planarity :  0.005   0.093   1586
  Dihedral  :  4.536  52.348   1242
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  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:  0.10 (0.26), residues: 1145
  helix:  0.94 (0.19), residues: 712
  sheet: -1.30 (0.58), residues: 75
  loop : -1.33 (0.36), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  35 
 HIS   0.003   0.001   HIS E  72 
 PHE   0.013   0.001   PHE E  47 
 TYR   0.027   0.001   TYR B 287 
 ARG   0.005   0.000   ARG A  76 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  238 ARG cc_start: 0.6670 (mmm160) cc_final: 0.5403 (mmm160)
REVERT: B  347 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6931 (tm-30)
REVERT: B  377 SER cc_start: 0.8561 (m) cc_final: 0.8299 (t)
REVERT: B  400 MET cc_start: 0.7954 (mtt) cc_final: 0.7743 (mtt)
REVERT: B  406 ARG cc_start: 0.7326 (mpt-90) cc_final: 0.6727 (mpt-90)
REVERT: A  248 SER cc_start: 0.9186 (p) cc_final: 0.8956 (t)
REVERT: A  521 LYS cc_start: 0.8859 (tptm) cc_final: 0.8279 (ttpt)
REVERT: A  562 ASP cc_start: 0.6645 (p0) cc_final: 0.6401 (p0)
REVERT: A  601 ASP cc_start: 0.7832 (m-30) cc_final: 0.7537 (m-30)
REVERT: E   46 MET cc_start: 0.7135 (ttm) cc_final: 0.6318 (tmm)
REVERT: E   54 LYS cc_start: 0.7942 (tttt) cc_final: 0.7426 (tmtt)
REVERT: E   75 TYR cc_start: 0.7625 (t80) cc_final: 0.7277 (t80)
REVERT: E  165 MET cc_start: 0.6222 (mmm) cc_final: 0.5786 (mpp)
REVERT: F  154 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6279 (ttp80)
REVERT: F  158 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8125 (mt-10)
REVERT: F  182 GLU cc_start: 0.7967 (tp30) cc_final: 0.7714 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.2078
  time to fit residues: 67.0378
Evaluate side-chains
  194 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 109 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 50 optimal weight:    0.0470
   chunk 7 optimal weight:    0.4980
   chunk 104 optimal weight:   10.0000
   chunk 112 optimal weight:    0.4980
   chunk 67 optimal weight:    6.9990
   chunk 58 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   overall best weight:    1.5280

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

Flipped N/Q/H residues before XYZ refinement:
B  48 GLN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 HIS ** 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 = 0.3658 r_free = 0.3658 target = 0.142920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.111306 restraints weight = 17245.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.113515 restraints weight = 11632.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.114840 restraints weight = 8928.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9366  Z= 0.193
  Angle     :  0.624  11.043  12685  Z= 0.308
  Chirality :  0.043   0.183   1493
  Planarity :  0.005   0.079   1586
  Dihedral  :  4.469  52.545   1242
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.24 (0.26), residues: 1145
  helix:  1.07 (0.19), residues: 712
  sheet: -1.32 (0.59), residues: 75
  loop : -1.28 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 159 
 HIS   0.004   0.001   HIS A 330 
 PHE   0.012   0.001   PHE E  66 
 TYR   0.018   0.001   TYR B 287 
 ARG   0.004   0.000   ARG A  76 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   48 GLN cc_start: 0.8282 (mm110) cc_final: 0.7711 (mp10)
REVERT: B   61 ASP cc_start: 0.6560 (p0) cc_final: 0.6303 (p0)
REVERT: B   85 ILE cc_start: 0.8903 (pt) cc_final: 0.8571 (tp)
REVERT: B  238 ARG cc_start: 0.6644 (mmm160) cc_final: 0.5507 (mmm160)
REVERT: B  249 MET cc_start: 0.8148 (mmm) cc_final: 0.7686 (mmm)
REVERT: B  377 SER cc_start: 0.8558 (m) cc_final: 0.8271 (t)
REVERT: B  400 MET cc_start: 0.7970 (mtt) cc_final: 0.7677 (mtm)
REVERT: B  406 ARG cc_start: 0.7284 (mpt-90) cc_final: 0.6753 (mpt-90)
REVERT: A  248 SER cc_start: 0.9163 (p) cc_final: 0.8952 (t)
REVERT: A  521 LYS cc_start: 0.8885 (tptm) cc_final: 0.8316 (ttpt)
REVERT: A  562 ASP cc_start: 0.6625 (p0) cc_final: 0.6410 (p0)
REVERT: A  601 ASP cc_start: 0.7611 (m-30) cc_final: 0.7336 (m-30)
REVERT: A  606 MET cc_start: 0.9075 (mtm) cc_final: 0.8808 (mtp)
REVERT: E   46 MET cc_start: 0.7133 (ttm) cc_final: 0.6296 (tmm)
REVERT: E   54 LYS cc_start: 0.7885 (tttt) cc_final: 0.7359 (tmtt)
REVERT: E   75 TYR cc_start: 0.7577 (t80) cc_final: 0.7247 (t80)
REVERT: E   99 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7695 (mmm-85)
REVERT: E  165 MET cc_start: 0.6208 (mmm) cc_final: 0.5845 (mpp)
REVERT: F  154 ARG cc_start: 0.7380 (mtp180) cc_final: 0.6329 (ttp80)
REVERT: F  158 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8158 (mt-10)
REVERT: F  182 GLU cc_start: 0.8068 (tp30) cc_final: 0.7682 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2077
  time to fit residues: 67.1733
Evaluate side-chains
  196 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 87 optimal weight:    0.4980
   chunk 72 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 106 optimal weight:    0.0570
   chunk 25 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0670
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:    0.3980
   chunk 103 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 HIS ** 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 = 0.3690 r_free = 0.3690 target = 0.145252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.114364 restraints weight = 16674.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116532 restraints weight = 11322.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.117953 restraints weight = 8726.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9366  Z= 0.157
  Angle     :  0.605  10.380  12685  Z= 0.298
  Chirality :  0.042   0.203   1493
  Planarity :  0.004   0.071   1586
  Dihedral  :  4.286  54.355   1242
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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:  0.47 (0.26), residues: 1145
  helix:  1.24 (0.19), residues: 712
  sheet: -1.24 (0.59), residues: 75
  loop : -1.17 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 159 
 HIS   0.005   0.001   HIS A 330 
 PHE   0.013   0.001   PHE E  66 
 TYR   0.014   0.001   TYR B 344 
 ARG   0.004   0.000   ARG A  76 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 1.084 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.6835 (p0) cc_final: 0.6552 (p0)
REVERT: B   85 ILE cc_start: 0.8912 (pt) cc_final: 0.8590 (tp)
REVERT: B  238 ARG cc_start: 0.6417 (mmm160) cc_final: 0.5479 (mmm160)
REVERT: B  380 TRP cc_start: 0.8902 (t-100) cc_final: 0.8275 (t-100)
REVERT: B  400 MET cc_start: 0.7761 (mtt) cc_final: 0.7216 (mtm)
REVERT: B  406 ARG cc_start: 0.7184 (mpt-90) cc_final: 0.6722 (mpt-90)
REVERT: A  336 LEU cc_start: 0.8703 (tp) cc_final: 0.8369 (tt)
REVERT: A  521 LYS cc_start: 0.8861 (tptm) cc_final: 0.8301 (ttpt)
REVERT: A  562 ASP cc_start: 0.6543 (p0) cc_final: 0.6243 (p0)
REVERT: A  601 ASP cc_start: 0.7498 (m-30) cc_final: 0.7135 (m-30)
REVERT: A  606 MET cc_start: 0.9043 (mtm) cc_final: 0.8793 (mtp)
REVERT: E   34 LEU cc_start: 0.8243 (tp) cc_final: 0.7958 (tp)
REVERT: E   46 MET cc_start: 0.7116 (ttm) cc_final: 0.6238 (tmm)
REVERT: E   54 LYS cc_start: 0.7841 (tttt) cc_final: 0.7377 (tmtt)
REVERT: E   75 TYR cc_start: 0.7587 (t80) cc_final: 0.7297 (t80)
REVERT: E   99 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7764 (mmm-85)
REVERT: F  154 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6158 (ttp80)
REVERT: F  158 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7934 (mt-10)
REVERT: F  172 GLU cc_start: 0.7216 (pp20) cc_final: 0.6907 (pp20)
REVERT: F  182 GLU cc_start: 0.7828 (tp30) cc_final: 0.7419 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2058
  time to fit residues: 67.6425
Evaluate side-chains
  194 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 87 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 32 optimal weight:    0.4980
   chunk 98 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 110 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
B  48 GLN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 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 = 0.3628 r_free = 0.3628 target = 0.140394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.109503 restraints weight = 16896.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.111649 restraints weight = 11562.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.112978 restraints weight = 8931.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9366  Z= 0.277
  Angle     :  0.686  12.066  12685  Z= 0.342
  Chirality :  0.045   0.172   1493
  Planarity :  0.005   0.073   1586
  Dihedral  :  4.562  52.368   1242
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  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:  0.31 (0.26), residues: 1145
  helix:  1.10 (0.19), residues: 712
  sheet: -1.14 (0.59), residues: 74
  loop : -1.25 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  35 
 HIS   0.005   0.001   HIS D  72 
 PHE   0.015   0.002   PHE E  47 
 TYR   0.028   0.002   TYR B 287 
 ARG   0.004   0.000   ARG A  76 

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6797 (p0) cc_final: 0.6510 (p0)
REVERT: B   85 ILE cc_start: 0.8914 (pt) cc_final: 0.8568 (tp)
REVERT: B  189 ILE cc_start: 0.9610 (mt) cc_final: 0.9404 (mt)
REVERT: B  238 ARG cc_start: 0.6723 (mmm160) cc_final: 0.5621 (mmm160)
REVERT: B  377 SER cc_start: 0.8642 (m) cc_final: 0.8373 (t)
REVERT: B  400 MET cc_start: 0.7989 (mtt) cc_final: 0.7774 (mtt)
REVERT: B  406 ARG cc_start: 0.7262 (mpt-90) cc_final: 0.6876 (mpt-90)
REVERT: A  521 LYS cc_start: 0.8910 (tptm) cc_final: 0.8355 (ttpt)
REVERT: A  562 ASP cc_start: 0.6590 (p0) cc_final: 0.6227 (p0)
REVERT: A  601 ASP cc_start: 0.7855 (m-30) cc_final: 0.7531 (m-30)
REVERT: A  606 MET cc_start: 0.9007 (mtm) cc_final: 0.8690 (mtp)
REVERT: E   46 MET cc_start: 0.7162 (ttm) cc_final: 0.6311 (tmm)
REVERT: E   54 LYS cc_start: 0.7907 (tttt) cc_final: 0.7357 (tmtt)
REVERT: E   75 TYR cc_start: 0.7640 (t80) cc_final: 0.7358 (t80)
REVERT: E  165 MET cc_start: 0.7143 (mpp) cc_final: 0.6749 (mmm)
REVERT: F  154 ARG cc_start: 0.7234 (mtp180) cc_final: 0.6351 (ttp80)
REVERT: F  158 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8015 (mt-10)
REVERT: F  182 GLU cc_start: 0.7839 (tp30) cc_final: 0.7479 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.2119
  time to fit residues: 65.7085
Evaluate side-chains
  189 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   chunk 20 optimal weight:    0.3980
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   overall best weight:    3.2788

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107975 restraints weight = 17085.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.110004 restraints weight = 11482.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.111145 restraints weight = 8882.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9366  Z= 0.304
  Angle     :  0.711  12.625  12685  Z= 0.351
  Chirality :  0.046   0.174   1493
  Planarity :  0.005   0.072   1586
  Dihedral  :  4.701  52.188   1242
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  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:  0.04 (0.25), residues: 1145
  helix:  0.94 (0.19), residues: 721
  sheet: -1.14 (0.59), residues: 74
  loop : -1.57 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  35 
 HIS   0.005   0.001   HIS E  72 
 PHE   0.016   0.002   PHE E  47 
 TYR   0.026   0.002   TYR B 287 
 ARG   0.004   0.000   ARG A  76 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2900.07 seconds
wall clock time: 52 minutes 56.01 seconds (3176.01 seconds total)