Starting phenix.real_space_refine
on Sat Nov 16 19:00:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggd_40003/11_2024/8ggd_40003.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggd_40003/11_2024/8ggd_40003.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggd_40003/11_2024/8ggd_40003.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggd_40003/11_2024/8ggd_40003.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggd_40003/11_2024/8ggd_40003.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggd_40003/11_2024/8ggd_40003.cif"
  }
  resolution = 3.33
  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=   0.019
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      68      5.16       5
     C    7432      2.51       5
     N    2060      2.21       5
     O    2164      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 11724
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2390
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 299}
    Chain: "B"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2390
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 299}
    Chain: "C"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2390
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 299}
    Chain: "A"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2390
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 299}
    Chain: "E"
      Number of atoms: 2164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2164
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 13, 'TRANS': 261}
          Chain breaks: 1
  Time building chain proxies: 8.62, per 1000 atoms: 0.74
  Number of scatterers: 11724
  At special positions: 0
  Unit cell: (103.2, 107.5, 133.3, 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      68     16.00
     O    2164      8.00
     N    2060      7.00
     C    7432      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2870

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 13 sheets defined
      51.6% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'D' and resid 11 through 22
      removed outlier: 3.515A  pdb=" N   GLN D  15 " --> pdb=" O   GLY D  11 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   SER D  16 " --> pdb=" O   GLY D  12 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 47
      removed outlier: 3.537A  pdb=" N   VAL D  42 " --> pdb=" O   GLY D  38 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP D  45 " --> pdb=" O   GLY D  41 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU D  46 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER D  47 " --> pdb=" O   ALA D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 76
    Processing helix  chain 'D' and resid 95 through 115
      removed outlier: 3.547A  pdb=" N   PHE D 100 " --> pdb=" O   ARG D  96 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ASN D 101 " --> pdb=" O   ASP D  97 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLY D 105 " --> pdb=" O   ASN D 101 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ILE D 106 " --> pdb=" O   VAL D 102 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU D 112 " --> pdb=" O   MET D 108 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR D 113 " --> pdb=" O   ASP D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 132
    Processing helix  chain 'D' and resid 133 through 145
    Processing helix  chain 'D' and resid 157 through 171
      removed outlier: 4.008A  pdb=" N   ALA D 163 " --> pdb=" O   ASP D 159 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA D 170 " --> pdb=" O   PHE D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 197
      removed outlier: 4.104A  pdb=" N   ILE D 197 " --> pdb=" O   TYR D 194 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 194 through 197'
    Processing helix  chain 'D' and resid 203 through 225
      removed outlier: 3.535A  pdb=" N   GLN D 215 " --> pdb=" O   ARG D 211 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   GLY D 218 " --> pdb=" O   VAL D 214 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   THR D 219 " --> pdb=" O   GLN D 215 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLU D 220 " --> pdb=" O   VAL D 216 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   VAL D 221 " --> pdb=" O   ALA D 217 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   VAL D 222 " --> pdb=" O   GLY D 218 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 251
      removed outlier: 3.505A  pdb=" N   ALA D 238 " --> pdb=" O   SER D 234 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY D 239 " --> pdb=" O   MET D 235 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA D 240 " --> pdb=" O   ALA D 236 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   MET D 244 " --> pdb=" O   ALA D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 294 through 322
      removed outlier: 3.607A  pdb=" N   LYS D 298 " --> pdb=" O   THR D 294 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   GLU D 299 " --> pdb=" O   THR D 295 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   MET D 300 " --> pdb=" O   VAL D 296 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS D 310 " --> pdb=" O   GLY D 306 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ALA D 319 " --> pdb=" O   GLY D 315 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   ARG D 320 " --> pdb=" O   GLU D 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 22
      removed outlier: 3.509A  pdb=" N   LEU B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 47
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 95 through 116
      removed outlier: 4.372A  pdb=" N   LEU B  99 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 145
      Proline residue:  B 135  - end of helix
    Processing helix  chain 'B' and resid 157 through 171
    Processing helix  chain 'B' and resid 204 through 225
      removed outlier: 5.572A  pdb=" N   GLY B 218 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   THR B 219 " --> pdb=" O   GLN B 215 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLU B 220 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL B 222 " --> pdb=" O   GLY B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 251
      removed outlier: 3.503A  pdb=" N   GLU B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA B 238 " --> pdb=" O   SER B 234 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLY B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA B 240 " --> pdb=" O   ALA B 236 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ARG B 241 " --> pdb=" O   GLU B 237 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   PHE B 242 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 320
      removed outlier: 3.669A  pdb=" N   MET B 300 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ARG B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 323
      No H-bonds generated for 'chain 'B' and resid 321 through 323'
    Processing helix  chain 'C' and resid 13 through 23
      removed outlier: 3.615A  pdb=" N   ARG C  23 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 47
    Processing helix  chain 'C' and resid 69 through 75
    Processing helix  chain 'C' and resid 99 through 116
      removed outlier: 4.359A  pdb=" N   GLY C 105 " --> pdb=" O   ASN C 101 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE C 106 " --> pdb=" O   VAL C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 145
      Proline residue:  C 135  - end of helix
      removed outlier: 3.585A  pdb=" N   ILE C 144 " --> pdb=" O   THR C 140 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY C 145 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 169
      removed outlier: 4.170A  pdb=" N   GLY C 160 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 197
      removed outlier: 4.328A  pdb=" N   ILE C 197 " --> pdb=" O   TYR C 194 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 194 through 197'
    Processing helix  chain 'C' and resid 203 through 216
    Processing helix  chain 'C' and resid 219 through 225
    Processing helix  chain 'C' and resid 234 through 252
    Processing helix  chain 'C' and resid 299 through 322
      removed outlier: 5.383A  pdb=" N   VAL C 305 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY C 306 " --> pdb=" O   GLU C 302 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS C 310 " --> pdb=" O   GLY C 306 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE C 318 " --> pdb=" O   LYS C 314 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ALA C 319 " --> pdb=" O   GLY C 315 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ARG C 320 " --> pdb=" O   GLU C 316 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   SER C 321 " --> pdb=" O   THR C 317 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LYS C 322 " --> pdb=" O   PHE C 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 23
      removed outlier: 3.616A  pdb=" N   ARG A  23 " --> pdb=" O   LEU A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 47
      removed outlier: 3.623A  pdb=" N   ASP A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 76
    Processing helix  chain 'A' and resid 95 through 116
      removed outlier: 4.173A  pdb=" N   LEU A  99 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASN A 101 " --> pdb=" O   ASP A  97 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ASP A 109 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   CYS A 114 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 145
      removed outlier: 3.858A  pdb=" N   ILE A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE A 144 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 4.126A  pdb=" N   LEU A 152 " --> pdb=" O   LYS A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 171
      removed outlier: 4.192A  pdb=" N   GLY A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   PHE A 166 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ILE A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   ASN A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ASN A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 170 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 216
      removed outlier: 4.205A  pdb=" N   GLU A 209 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 225
      removed outlier: 3.712A  pdb=" N   VAL A 221 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 252
      removed outlier: 3.716A  pdb=" N   GLU A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ALA A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 316
      removed outlier: 4.515A  pdb=" N   MET A 300 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 338 through 344
    Processing helix  chain 'E' and resid 354 through 359
    Processing helix  chain 'E' and resid 362 through 373
      removed outlier: 4.051A  pdb=" N   LEU E 370 " --> pdb=" O   GLY E 366 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   GLN E 371 " --> pdb=" O   ILE E 367 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU E 372 " --> pdb=" O   ALA E 368 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 376 through 387
      removed outlier: 3.744A  pdb=" N   LEU E 380 " --> pdb=" O   ALA E 376 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 392 through 406
      removed outlier: 4.079A  pdb=" N   THR E 401 " --> pdb=" O   ARG E 397 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA E 404 " --> pdb=" O   GLY E 400 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLU E 405 " --> pdb=" O   THR E 401 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ASN E 406 " --> pdb=" O   THR E 402 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 413 through 423
    Processing helix  chain 'E' and resid 427 through 438
      removed outlier: 3.711A  pdb=" N   ALA E 434 " --> pdb=" O   HIS E 430 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   VAL E 435 " --> pdb=" O   ALA E 431 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER E 436 " --> pdb=" O   ALA E 432 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 444 through 456
      removed outlier: 4.061A  pdb=" N   GLN E 448 " --> pdb=" O   GLY E 444 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 492 through 502
      removed outlier: 3.849A  pdb=" N   ALA E 502 " --> pdb=" O   THR E 498 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 510 through 523
      removed outlier: 3.781A  pdb=" N   LEU E 517 " --> pdb=" O   LEU E 513 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   GLY E 518 " --> pdb=" O   HIS E 514 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL E 519 " --> pdb=" O   ALA E 515 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 526 through 541
      removed outlier: 4.001A  pdb=" N   ALA E 531 " --> pdb=" O   PHE E 527 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LYS E 532 " --> pdb=" O   ASP E 528 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG E 536 " --> pdb=" O   LYS E 532 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU E 539 " --> pdb=" O   ARG E 535 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ARG E 541 " --> pdb=" O   ALA E 537 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 544 through 557
      removed outlier: 4.017A  pdb=" N   TRP E 548 " --> pdb=" O   ASP E 544 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU E 555 " --> pdb=" O   LEU E 551 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 564 through 575
      removed outlier: 3.536A  pdb=" N   LEU E 572 " --> pdb=" O   TYR E 568 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASP E 573 " --> pdb=" O   ASN E 569 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE E 574 " --> pdb=" O   ARG E 570 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASN E 575 " --> pdb=" O   ALA E 571 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 578 through 592
      removed outlier: 3.564A  pdb=" N   MET E 582 " --> pdb=" O   TYR E 578 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 598 through 610
      removed outlier: 5.302A  pdb=" N   ARG E 604 " --> pdb=" O   LYS E 600 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA E 610 " --> pdb=" O   ILE E 606 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 614 through 618
    Processing helix  chain 'E' and resid 624 through 638
      removed outlier: 3.555A  pdb=" N   TRP E 628 " --> pdb=" O   THR E 624 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU E 631 " --> pdb=" O   LEU E 627 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG E 632 " --> pdb=" O   TRP E 628 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 57 through 58
      removed outlier: 6.872A  pdb=" N   VAL D   4 " --> pdb=" O   SER D  32 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   TYR D  34 " --> pdb=" O   VAL D   4 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL D   6 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   PHE D  82 " --> pdb=" O   CYS D 124 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   PHE D 123 " --> pdb=" O   LEU D 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 181 through 183
    Processing sheet with id=AA3, first strand: chain 'D' and resid 257 through 263
      removed outlier: 4.032A  pdb=" N   ALA D 260 " --> pdb=" O   MET D 275 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   MET D 275 " --> pdb=" O   ALA D 260 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL D 278 " --> pdb=" O   GLU D 285 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7
    Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 35
      removed outlier: 3.911A  pdb=" N   ASP B  35 " --> pdb=" O   ALA B  59 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183
    Processing sheet with id=AA7, first strand: chain 'B' and resid 257 through 262
      removed outlier: 3.915A  pdb=" N   ALA B 260 " --> pdb=" O   MET B 275 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   MET B 275 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU B 273 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   ARG B 287 " --> pdb=" O   PRO B 276 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   VAL B 278 " --> pdb=" O   GLU B 285 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLY B 283 " --> pdb=" O   GLY B 280 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 54 through 60
      removed outlier: 3.689A  pdb=" N   THR C  55 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASP C  35 " --> pdb=" O   ALA C  59 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   PHE C 123 " --> pdb=" O   LEU C 153 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 181 through 183
    Processing sheet with id=AB1, first strand: chain 'C' and resid 257 through 259
      removed outlier: 3.856A  pdb=" N   ARG C 286 " --> pdb=" O   VAL C 278 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 56 through 59
      removed outlier: 6.278A  pdb=" N   LEU A  31 " --> pdb=" O   LYS A  57 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   ALA A  59 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LEU A  33 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL A   4 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   TYR A  34 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   VAL A   6 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 181 through 182
    Processing sheet with id=AB4, first strand: chain 'A' and resid 257 through 258
      removed outlier: 3.861A  pdb=" N   ARG A 286 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)

    509 hydrogen bonds defined for protein.
    1488 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: 3.74

  Time building geometry restraints manager: 3.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3004
        1.33 -     1.45: 1854
        1.45 -     1.57: 6961
        1.57 -     1.70: 1
        1.70 -     1.82: 116
  Bond restraints: 11936
  Sorted by residual:
  bond pdb=" C   LEU C  63 "
       pdb=" N   PRO C  64 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.18e-02 7.18e+03 8.09e+00
  bond pdb=" N   TYR E 595 "
       pdb=" CA  TYR E 595 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.13e-02 7.83e+03 7.47e+00
  bond pdb=" N   THR A 317 "
       pdb=" CA  THR A 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.00e-02 1.00e+04 7.46e+00
  bond pdb=" CA  ARG D 171 "
       pdb=" C   ARG D 171 "
    ideal  model  delta    sigma   weight residual
    1.523  1.487  0.037 1.34e-02 5.57e+03 7.45e+00
  bond pdb=" N   ILE A 144 "
       pdb=" CA  ILE A 144 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.32e+00
  ... (remaining 11931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 15935
        2.43 -     4.85: 271
        4.85 -     7.28: 28
        7.28 -     9.70: 7
        9.70 -    12.13: 4
  Bond angle restraints: 16245
  Sorted by residual:
  angle pdb=" N   ASN A 131 "
        pdb=" CA  ASN A 131 "
        pdb=" C   ASN A 131 "
      ideal   model   delta    sigma   weight residual
     113.41  103.68    9.73 1.22e+00 6.72e-01 6.36e+01
  angle pdb=" C   HIS D 172 "
        pdb=" N   PRO D 173 "
        pdb=" CA  PRO D 173 "
      ideal   model   delta    sigma   weight residual
     119.56  113.91    5.65 1.01e+00 9.80e-01 3.12e+01
  angle pdb=" N   CYS E 410 "
        pdb=" CA  CYS E 410 "
        pdb=" C   CYS E 410 "
      ideal   model   delta    sigma   weight residual
     114.62  108.72    5.90 1.14e+00 7.69e-01 2.68e+01
  angle pdb=" N   ILE A  13 "
        pdb=" CA  ILE A  13 "
        pdb=" C   ILE A  13 "
      ideal   model   delta    sigma   weight residual
     112.29  107.43    4.86 9.40e-01 1.13e+00 2.67e+01
  angle pdb=" N   GLY C  61 "
        pdb=" CA  GLY C  61 "
        pdb=" C   GLY C  61 "
      ideal   model   delta    sigma   weight residual
     113.18  125.31  -12.13 2.37e+00 1.78e-01 2.62e+01
  ... (remaining 16240 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6573
       17.99 -    35.98: 575
       35.98 -    53.97: 124
       53.97 -    71.96: 23
       71.96 -    89.95: 8
  Dihedral angle restraints: 7303
    sinusoidal: 2837
      harmonic: 4466
  Sorted by residual:
  dihedral pdb=" CA  HIS A 172 "
           pdb=" C   HIS A 172 "
           pdb=" N   PRO A 173 "
           pdb=" CA  PRO A 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.06   28.94     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  LEU C 301 "
           pdb=" C   LEU C 301 "
           pdb=" N   GLU C 302 "
           pdb=" CA  GLU C 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.92   23.08     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  HIS E 359 "
           pdb=" C   HIS E 359 "
           pdb=" N   ASP E 360 "
           pdb=" CA  ASP E 360 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.55   22.45     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 7300 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1491
       0.050 -    0.100: 332
       0.100 -    0.149: 108
       0.149 -    0.199: 9
       0.199 -    0.249: 4
  Chirality restraints: 1944
  Sorted by residual:
  chirality pdb=" CA  HIS D 172 "
            pdb=" N   HIS D 172 "
            pdb=" C   HIS D 172 "
            pdb=" CB  HIS D 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  PRO E 615 "
            pdb=" N   PRO E 615 "
            pdb=" C   PRO E 615 "
            pdb=" CB  PRO E 615 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  LEU E 597 "
            pdb=" N   LEU E 597 "
            pdb=" C   LEU E 597 "
            pdb=" CB  LEU E 597 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1941 not shown)

  Planarity restraints: 2110
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E 614 "   -0.078 5.00e-02 4.00e+02   1.19e-01 2.26e+01
        pdb=" N   PRO E 615 "    0.205 5.00e-02 4.00e+02
        pdb=" CA  PRO E 615 "   -0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO E 615 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  63 "    0.071 5.00e-02 4.00e+02   1.05e-01 1.78e+01
        pdb=" N   PRO C  64 "   -0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO C  64 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO C  64 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 128 "   -0.069 5.00e-02 4.00e+02   1.02e-01 1.66e+01
        pdb=" N   PRO A 129 "    0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO A 129 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 129 "   -0.057 5.00e-02 4.00e+02
  ... (remaining 2107 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1897
        2.76 -     3.30: 11495
        3.30 -     3.83: 18182
        3.83 -     4.37: 20174
        4.37 -     4.90: 35976
  Nonbonded interactions: 87724
  Sorted by model distance:
  nonbonded pdb=" O   ALA E 335 "
            pdb=" NE2 GLN E 338 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   GLU E 618 "
            pdb=" NH1 ARG E 621 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" OH  TYR B 147 "
            pdb=" OD2 ASP B 263 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OH  TYR E 568 "
            pdb=" OD1 ASN E 584 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OXT LEU A 323 "
            pdb=" ND2 ASN E 439 "
     model   vdw
     2.246 3.120
  ... (remaining 87719 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.730
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     28.920
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
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      :  0.004   0.087  11936  Z= 0.266
  Angle     :  0.741  12.131  16245  Z= 0.435
  Chirality :  0.048   0.249   1944
  Planarity :  0.006   0.119   2110
  Dihedral  : 14.509  89.953   4433
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  1.35 %
    Allowed  : 11.00 %
    Favored  : 87.65 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  :  0.87 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.22), residues: 1555
  helix:  0.44 (0.21), residues: 727
  sheet: -1.96 (0.41), residues: 172
  loop : -2.29 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E 548 
 HIS   0.003   0.001   HIS D 172 
 PHE   0.017   0.001   PHE E 350 
 TYR   0.033   0.001   TYR E 595 
 ARG   0.003   0.000   ARG B 211 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 147
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 PRO cc_start: 0.8860 (Cg_exo) cc_final: 0.8476 (Cg_endo)
REVERT: A  235 MET cc_start: 0.7992 (ttm) cc_final: 0.7575 (tpp)
REVERT: E  425 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7920 (tptt)
REVERT: E  501 TYR cc_start: 0.7075 (m-10) cc_final: 0.6623 (m-80)
REVERT: E  591 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7089 (p0)
  outliers start: 35
  outliers final: 8
  residues processed: 171
  average time/residue: 0.2450
  time to fit residues: 60.0426
Evaluate side-chains
  113 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  167 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain E residue  407 GLU
Chi-restraints excluded: chain E residue  500 LEU
Chi-restraints excluded: chain E residue  591 ASN
Chi-restraints excluded: chain E residue  594 GLN
Chi-restraints excluded: chain E residue  631 LEU
Chi-restraints excluded: chain E residue  634 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 121 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9980
   chunk 140 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
E 374 ASN
** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 557 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  11936  Z= 0.273
  Angle     :  0.655  11.703  16245  Z= 0.333
  Chirality :  0.045   0.211   1944
  Planarity :  0.007   0.121   2110
  Dihedral  :  5.968  59.449   1700
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 10.16 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  7.97 %
    Favored  : 90.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.95 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.22), residues: 1555
  helix:  0.72 (0.20), residues: 743
  sheet: -1.70 (0.38), residues: 202
  loop : -2.51 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 548 
 HIS   0.005   0.001   HIS E 437 
 PHE   0.022   0.002   PHE C 100 
 TYR   0.014   0.002   TYR A 259 
 ARG   0.005   0.000   ARG E 625 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.6753 (tmm) cc_final: 0.6160 (tmm)
REVERT: B  194 TYR cc_start: 0.8327 (m-10) cc_final: 0.8100 (m-80)
REVERT: E  425 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7904 (tptt)
REVERT: E  436 SER cc_start: 0.8908 (m) cc_final: 0.8530 (t)
REVERT: E  559 ASN cc_start: 0.7642 (p0) cc_final: 0.7271 (t0)
REVERT: E  591 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7482 (p0)
REVERT: E  592 MET cc_start: 0.8250 (tpp) cc_final: 0.7521 (ppp)
REVERT: E  594 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6656 (mp10)
  outliers start: 18
  outliers final: 13
  residues processed: 132
  average time/residue: 0.2399
  time to fit residues: 46.0228
Evaluate side-chains
  122 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  156 SER
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  167 ILE
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain E residue  438 THR
Chi-restraints excluded: chain E residue  500 LEU
Chi-restraints excluded: chain E residue  504 VAL
Chi-restraints excluded: chain E residue  591 ASN
Chi-restraints excluded: chain E residue  594 GLN
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 141 optimal weight:    4.9990
   chunk 152 optimal weight:    7.9990
   chunk 125 optimal weight:    0.0570
   chunk 139 optimal weight:    6.9990
   chunk 48 optimal weight:    0.4980
   chunk 113 optimal weight:    0.5980
   overall best weight:    1.0302

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

Flipped N/Q/H residues before XYZ refinement:
D 311 ASN
** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  11936  Z= 0.233
  Angle     :  0.590   8.524  16245  Z= 0.300
  Chirality :  0.043   0.213   1944
  Planarity :  0.007   0.124   2110
  Dihedral  :  5.435  59.833   1694
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  9.39 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.87 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    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: -0.93 (0.22), residues: 1555
  helix:  1.01 (0.20), residues: 747
  sheet: -1.68 (0.40), residues: 182
  loop : -2.35 (0.24), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 548 
 HIS   0.004   0.001   HIS A 172 
 PHE   0.014   0.001   PHE C 100 
 TYR   0.012   0.001   TYR A 259 
 ARG   0.004   0.000   ARG E 625 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
REVERT: D  317 THR cc_start: 0.8678 (m) cc_final: 0.8446 (t)
REVERT: B  194 TYR cc_start: 0.8386 (m-10) cc_final: 0.8157 (m-80)
REVERT: E  425 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7872 (tptt)
REVERT: E  436 SER cc_start: 0.8913 (m) cc_final: 0.8575 (t)
REVERT: E  495 ASP cc_start: 0.8161 (m-30) cc_final: 0.7891 (p0)
REVERT: E  559 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7260 (t0)
REVERT: E  591 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7563 (p0)
REVERT: E  592 MET cc_start: 0.8305 (tpp) cc_final: 0.7745 (ppp)
REVERT: E  594 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7194 (mp10)
  outliers start: 20
  outliers final: 9
  residues processed: 129
  average time/residue: 0.2293
  time to fit residues: 43.4834
Evaluate side-chains
  120 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain E residue  435 VAL
Chi-restraints excluded: chain E residue  504 VAL
Chi-restraints excluded: chain E residue  559 ASN
Chi-restraints excluded: chain E residue  591 ASN
Chi-restraints excluded: chain E residue  594 GLN
Chi-restraints excluded: chain E residue  597 LEU
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 139 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 141 optimal weight:   10.0000
   chunk 149 optimal weight:    0.8980
   chunk 134 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  11936  Z= 0.261
  Angle     :  0.601   8.444  16245  Z= 0.305
  Chirality :  0.044   0.214   1944
  Planarity :  0.007   0.124   2110
  Dihedral  :  5.179  57.078   1689
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  9.65 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.23 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.22), residues: 1555
  helix:  1.07 (0.20), residues: 749
  sheet: -1.73 (0.39), residues: 182
  loop : -2.35 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP E 548 
 HIS   0.005   0.001   HIS A 172 
 PHE   0.028   0.001   PHE C 100 
 TYR   0.016   0.001   TYR A 259 
 ARG   0.006   0.000   ARG E 570 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 1.441 
Fit side-chains
REVERT: D  157 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8397 (tt)
REVERT: D  317 THR cc_start: 0.8683 (m) cc_final: 0.8454 (t)
REVERT: E  425 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7856 (tptt)
REVERT: E  436 SER cc_start: 0.8930 (m) cc_final: 0.8632 (t)
REVERT: E  495 ASP cc_start: 0.8179 (m-30) cc_final: 0.7907 (p0)
REVERT: E  559 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7223 (t0)
REVERT: E  592 MET cc_start: 0.8353 (tpp) cc_final: 0.7876 (ppp)
REVERT: E  613 THR cc_start: 0.7089 (p) cc_final: 0.6764 (p)
  outliers start: 22
  outliers final: 14
  residues processed: 125
  average time/residue: 0.2397
  time to fit residues: 43.9342
Evaluate side-chains
  114 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain E residue  410 CYS
Chi-restraints excluded: chain E residue  435 VAL
Chi-restraints excluded: chain E residue  504 VAL
Chi-restraints excluded: chain E residue  559 ASN
Chi-restraints excluded: chain E residue  591 ASN
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 127 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 134 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  11936  Z= 0.254
  Angle     :  0.596   7.957  16245  Z= 0.302
  Chirality :  0.043   0.214   1944
  Planarity :  0.007   0.125   2110
  Dihedral  :  4.860  52.082   1684
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  9.45 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.42 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    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: -0.80 (0.22), residues: 1555
  helix:  1.18 (0.20), residues: 747
  sheet: -1.72 (0.39), residues: 182
  loop : -2.34 (0.24), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 548 
 HIS   0.004   0.001   HIS A 172 
 PHE   0.019   0.001   PHE C 100 
 TYR   0.015   0.001   TYR A 259 
 ARG   0.003   0.000   ARG B 211 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 1.334 
Fit side-chains
REVERT: D  157 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8404 (tt)
REVERT: D  317 THR cc_start: 0.8692 (m) cc_final: 0.8459 (t)
REVERT: E  425 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7877 (tptt)
REVERT: E  436 SER cc_start: 0.8928 (m) cc_final: 0.8639 (t)
REVERT: E  495 ASP cc_start: 0.8205 (m-30) cc_final: 0.7914 (p0)
REVERT: E  592 MET cc_start: 0.8412 (tpp) cc_final: 0.7887 (ppp)
  outliers start: 27
  outliers final: 15
  residues processed: 126
  average time/residue: 0.2411
  time to fit residues: 44.5695
Evaluate side-chains
  116 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain E residue  410 CYS
Chi-restraints excluded: chain E residue  435 VAL
Chi-restraints excluded: chain E residue  504 VAL
Chi-restraints excluded: chain E residue  591 ASN
Chi-restraints excluded: chain E residue  597 LEU
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 134 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 149 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 144 optimal weight:    8.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  11936  Z= 0.302
  Angle     :  0.643  12.232  16245  Z= 0.321
  Chirality :  0.044   0.216   1944
  Planarity :  0.007   0.125   2110
  Dihedral  :  4.945  48.847   1684
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 10.03 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.36 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.22), residues: 1555
  helix:  1.11 (0.20), residues: 749
  sheet: -1.82 (0.39), residues: 182
  loop : -2.38 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 548 
 HIS   0.006   0.001   HIS A 172 
 PHE   0.017   0.001   PHE C 100 
 TYR   0.019   0.001   TYR A 259 
 ARG   0.004   0.000   ARG C  68 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 1.383 
Fit side-chains
REVERT: D  157 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8411 (tt)
REVERT: D  317 THR cc_start: 0.8696 (m) cc_final: 0.8480 (t)
REVERT: B    1 MET cc_start: 0.6673 (tmm) cc_final: 0.6139 (tmm)
REVERT: E  359 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6838 (t70)
REVERT: E  361 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7202 (ptpt)
REVERT: E  425 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7888 (tptt)
REVERT: E  436 SER cc_start: 0.8957 (m) cc_final: 0.8697 (t)
REVERT: E  538 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8481 (m)
REVERT: E  559 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7126 (t0)
REVERT: E  592 MET cc_start: 0.8448 (tpp) cc_final: 0.7866 (ppp)
  outliers start: 30
  outliers final: 20
  residues processed: 121
  average time/residue: 0.2423
  time to fit residues: 43.4817
Evaluate side-chains
  119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain E residue  337 GLU
Chi-restraints excluded: chain E residue  359 HIS
Chi-restraints excluded: chain E residue  410 CYS
Chi-restraints excluded: chain E residue  435 VAL
Chi-restraints excluded: chain E residue  504 VAL
Chi-restraints excluded: chain E residue  538 VAL
Chi-restraints excluded: chain E residue  559 ASN
Chi-restraints excluded: chain E residue  589 TYR
Chi-restraints excluded: chain E residue  591 ASN
Chi-restraints excluded: chain E residue  597 LEU
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 126 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 149 optimal weight:    5.9990
   chunk 93 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 92 optimal weight:    0.4980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  11936  Z= 0.211
  Angle     :  0.594  11.777  16245  Z= 0.296
  Chirality :  0.043   0.213   1944
  Planarity :  0.006   0.125   2110
  Dihedral  :  4.676  42.638   1684
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  8.94 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.68 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    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: -0.62 (0.23), residues: 1555
  helix:  1.35 (0.20), residues: 749
  sheet: -1.70 (0.39), residues: 182
  loop : -2.27 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 548 
 HIS   0.002   0.001   HIS A  48 
 PHE   0.017   0.001   PHE C 100 
 TYR   0.010   0.001   TYR A 259 
 ARG   0.002   0.000   ARG E 625 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 1.383 
Fit side-chains
REVERT: C  308 VAL cc_start: 0.7141 (OUTLIER) cc_final: 0.6934 (p)
REVERT: E  359 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6867 (t70)
REVERT: E  425 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7895 (tptt)
REVERT: E  436 SER cc_start: 0.8947 (m) cc_final: 0.8680 (t)
REVERT: E  538 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8432 (m)
REVERT: E  592 MET cc_start: 0.8388 (tpp) cc_final: 0.7818 (ppp)
  outliers start: 28
  outliers final: 15
  residues processed: 129
  average time/residue: 0.2375
  time to fit residues: 45.1949
Evaluate side-chains
  118 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain E residue  359 HIS
Chi-restraints excluded: chain E residue  435 VAL
Chi-restraints excluded: chain E residue  538 VAL
Chi-restraints excluded: chain E residue  559 ASN
Chi-restraints excluded: chain E residue  589 TYR
Chi-restraints excluded: chain E residue  591 ASN
Chi-restraints excluded: chain E residue  597 LEU
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   chunk 73 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 117 optimal weight:    0.5980
   chunk 135 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 437 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  11936  Z= 0.220
  Angle     :  0.630  13.548  16245  Z= 0.306
  Chirality :  0.043   0.211   1944
  Planarity :  0.006   0.124   2110
  Dihedral  :  4.597  39.160   1684
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  9.00 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.15 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    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: -0.54 (0.23), residues: 1555
  helix:  1.42 (0.20), residues: 752
  sheet: -1.66 (0.39), residues: 182
  loop : -2.27 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 548 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.015   0.001   PHE C 100 
 TYR   0.011   0.001   TYR D 147 
 ARG   0.002   0.000   ARG A  90 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 1.177 
Fit side-chains
REVERT: C  308 VAL cc_start: 0.7141 (OUTLIER) cc_final: 0.6928 (p)
REVERT: E  359 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6784 (t70)
REVERT: E  425 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7899 (tptt)
REVERT: E  436 SER cc_start: 0.8960 (m) cc_final: 0.8684 (t)
REVERT: E  538 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8443 (m)
REVERT: E  592 MET cc_start: 0.8423 (tpp) cc_final: 0.7635 (ppp)
  outliers start: 24
  outliers final: 15
  residues processed: 121
  average time/residue: 0.2444
  time to fit residues: 43.3549
Evaluate side-chains
  115 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain C residue  294 THR
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain E residue  359 HIS
Chi-restraints excluded: chain E residue  435 VAL
Chi-restraints excluded: chain E residue  538 VAL
Chi-restraints excluded: chain E residue  559 ASN
Chi-restraints excluded: chain E residue  589 TYR
Chi-restraints excluded: chain E residue  591 ASN
Chi-restraints excluded: chain E residue  597 LEU
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 143 optimal weight:    6.9990
   chunk 130 optimal weight:    4.9990
   chunk 139 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 109 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 125 optimal weight:    0.0970
   chunk 131 optimal weight:    0.7980
   chunk 138 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 437 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  11936  Z= 0.214
  Angle     :  0.629  12.946  16245  Z= 0.305
  Chirality :  0.043   0.210   1944
  Planarity :  0.006   0.124   2110
  Dihedral  :  4.500  34.102   1684
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  8.87 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.15 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    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: -0.44 (0.23), residues: 1555
  helix:  1.47 (0.20), residues: 762
  sheet: -1.59 (0.40), residues: 182
  loop : -2.23 (0.25), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 548 
 HIS   0.002   0.001   HIS E 437 
 PHE   0.015   0.001   PHE C 100 
 TYR   0.010   0.001   TYR D 147 
 ARG   0.004   0.000   ARG A 228 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 1.646 
Fit side-chains
REVERT: C  308 VAL cc_start: 0.7135 (OUTLIER) cc_final: 0.6921 (p)
REVERT: E  359 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.6798 (t70)
REVERT: E  425 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7885 (tptt)
REVERT: E  436 SER cc_start: 0.8893 (m) cc_final: 0.8620 (t)
REVERT: E  437 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.7002 (m-70)
REVERT: E  538 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8453 (m)
REVERT: E  585 MET cc_start: 0.8259 (mtt) cc_final: 0.8015 (mtt)
REVERT: E  592 MET cc_start: 0.8372 (tpp) cc_final: 0.7640 (ppp)
  outliers start: 23
  outliers final: 14
  residues processed: 129
  average time/residue: 0.2314
  time to fit residues: 44.8202
Evaluate side-chains
  121 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain C residue  294 THR
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain E residue  359 HIS
Chi-restraints excluded: chain E residue  435 VAL
Chi-restraints excluded: chain E residue  437 HIS
Chi-restraints excluded: chain E residue  523 LEU
Chi-restraints excluded: chain E residue  538 VAL
Chi-restraints excluded: chain E residue  559 ASN
Chi-restraints excluded: chain E residue  589 TYR
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 147 optimal weight:    5.9990
   chunk 89 optimal weight:    0.3980
   chunk 69 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0040
   chunk 154 optimal weight:    1.9990
   chunk 142 optimal weight:    3.9990
   chunk 122 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.2798

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

Flipped N/Q/H residues before XYZ refinement:
D 311 ASN
** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  11936  Z= 0.258
  Angle     :  0.658  14.190  16245  Z= 0.320
  Chirality :  0.044   0.210   1944
  Planarity :  0.007   0.124   2110
  Dihedral  :  4.503  32.521   1682
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  9.20 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 18.78 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    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: -0.50 (0.23), residues: 1555
  helix:  1.43 (0.20), residues: 763
  sheet: -1.67 (0.39), residues: 182
  loop : -2.26 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 548 
 HIS   0.004   0.001   HIS A 172 
 PHE   0.013   0.001   PHE C 100 
 TYR   0.014   0.001   TYR A 259 
 ARG   0.003   0.000   ARG A 228 

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.431 
Fit side-chains
REVERT: C  308 VAL cc_start: 0.7127 (OUTLIER) cc_final: 0.6896 (p)
REVERT: E  425 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7903 (tptt)
REVERT: E  538 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8461 (m)
REVERT: E  585 MET cc_start: 0.8312 (mtt) cc_final: 0.8062 (mtt)
  outliers start: 20
  outliers final: 15
  residues processed: 116
  average time/residue: 0.2405
  time to fit residues: 41.5212
Evaluate side-chains
  114 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  216 VAL
Chi-restraints excluded: chain D residue  251 MET
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue  294 THR
Chi-restraints excluded: chain C residue  308 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain E residue  435 VAL
Chi-restraints excluded: chain E residue  523 LEU
Chi-restraints excluded: chain E residue  538 VAL
Chi-restraints excluded: chain E residue  559 ASN
Chi-restraints excluded: chain E residue  589 TYR
Chi-restraints excluded: chain E residue  629 ASP
Chi-restraints excluded: chain E residue  630 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 123 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 126 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 108 optimal weight:    8.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
D 311 ASN
** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 437 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 = 0.3644 r_free = 0.3644 target = 0.112166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.085929 restraints weight = 24504.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 3.06
r_work: 0.3111 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  11936  Z= 0.225
  Angle     :  0.649  17.664  16245  Z= 0.312
  Chirality :  0.043   0.209   1944
  Planarity :  0.006   0.123   2110
  Dihedral  :  4.451  32.289   1682
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  8.87 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.10 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.90 %
    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: -0.42 (0.23), residues: 1555
  helix:  1.50 (0.20), residues: 762
  sheet: -1.61 (0.40), residues: 182
  loop : -2.23 (0.25), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 548 
 HIS   0.002   0.001   HIS A 172 
 PHE   0.014   0.001   PHE C 100 
 TYR   0.011   0.001   TYR D 147 
 ARG   0.002   0.000   ARG A 228 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2275.18 seconds
wall clock time: 46 minutes 17.23 seconds (2777.23 seconds total)