Starting phenix.real_space_refine
on Wed Jul 30 03:10:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e14_8953/07_2025/6e14_8953.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e14_8953/07_2025/6e14_8953.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e14_8953/07_2025/6e14_8953.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e14_8953/07_2025/6e14_8953.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e14_8953/07_2025/6e14_8953.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e14_8953/07_2025/6e14_8953.cif"
  }
  resolution = 4.0
  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=   0.001 sd=   0.010
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      37      5.16       5
     C    7508      2.51       5
     N    2078      2.21       5
     O    2372      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11995
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 2051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2051
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 16, 'TRANS': 262}
    Chain: "D"
      Number of atoms: 6167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 805, 6167
          Classifications: {'peptide': 805}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 31, 'TRANS': 773}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "F"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1137
          Classifications: {'peptide': 154}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 145}
    Chain: "G"
      Number of atoms: 1038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1038
          Classifications: {'peptide': 143}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 139}
    Chain: "C"
      Number of atoms: 1602
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 205, 1598
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 190}
      Conformer: "B"
        Number of residues, atoms: 205, 1598
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 190}
          bond proxies already assigned to first conformer: 1623
  Time building chain proxies: 7.93, per 1000 atoms: 0.66
  Number of scatterers: 11995
  At special positions: 0
  Unit cell: (92.65, 104.64, 200.56, 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      37     16.00
     O    2372      8.00
     N    2078      7.00
     C    7508      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H   3 " - pdb=" SG  CYS H  44 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 161 " - pdb=" SG  CYS H 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  63 " - pdb=" SG  CYS D  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 810 " - pdb=" SG  CYS D 832 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  16 " - pdb=" SG  CYS F  56 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  16 " - pdb=" SG  CYS G  54 " distance=2.03

  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: 2.96
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2888

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 30 sheets defined
      2.1% alpha, 35.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.99
  Creating SS restraints...
    Processing helix  chain 'D' and resid 19 through 24
      removed outlier: 4.644A  pdb=" N   GLU D  23 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASN D  24 " --> pdb=" O   SER D  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 19 through 24'
    Processing helix  chain 'D' and resid 92 through 97
    Processing helix  chain 'D' and resid 246 through 250
      removed outlier: 3.624A  pdb=" N   ARG D 250 " --> pdb=" O   ASP D 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 443 through 449
      removed outlier: 3.856A  pdb=" N   THR D 447 " --> pdb=" O   ASN D 443 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR D 448 " --> pdb=" O   PHE D 444 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 108 through 112
      removed outlier: 3.651A  pdb=" N   ALA F 111 " --> pdb=" O   PRO F 108 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LEU F 112 " --> pdb=" O   SER F 109 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 108 through 112'
    Processing helix  chain 'C' and resid 123 through 127
      removed outlier: 3.756A  pdb=" N   GLN C 126 " --> pdb=" O   PRO C 123 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA C 127 " --> pdb=" O   PRO C 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 123 through 127'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 2 through 4
      removed outlier: 3.557A  pdb=" N   PHE H  43 " --> pdb=" O   LYS H   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 19 through 21
      removed outlier: 6.575A  pdb=" N   VAL H  20 " --> pdb=" O   TYR H 149 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE H 142 " --> pdb=" O   GLN H 133 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLN H 133 " --> pdb=" O   PHE H 142 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   PHE H 144 " --> pdb=" O   LEU H 131 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU H 129 " --> pdb=" O   TRP H 146 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL H  56 " --> pdb=" O   VAL H  93 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL H  93 " --> pdb=" O   VAL H  56 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 33 through 37
      removed outlier: 6.040A  pdb=" N   LEU H  34 " --> pdb=" O   LEU H 109 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU H 109 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL H  36 " --> pdb=" O   LEU H 107 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   THR H  74 " --> pdb=" O   TYR H 108 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   GLY H  73 " --> pdb=" O   PHE H  84 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 117 through 118
    Processing sheet with id=AA5, first strand: chain 'H' and resid 161 through 163
      removed outlier: 3.658A  pdb=" N   VAL H 248 " --> pdb=" O   VAL H 185 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 167 through 171
      removed outlier: 6.463A  pdb=" N   VAL H 168 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   ASN G   8 " --> pdb=" O   VAL H 168 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   VAL H 170 " --> pdb=" O   ASN G   8 " (cutoff:3.500A)
      removed outlier: 8.825A  pdb=" N   LYS G  10 " --> pdb=" O   VAL H 170 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE H 272 " --> pdb=" O   ILE G   5 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   VAL G   7 " --> pdb=" O   SER H 270 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER H 270 " --> pdb=" O   VAL G   7 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   GLY H 273 " --> pdb=" O   SER H 198 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   SER H 198 " --> pdb=" O   GLY H 273 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 179 through 180
      removed outlier: 4.367A  pdb=" N   VAL H 179 " --> pdb=" O   ALA H 254 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA H 254 " --> pdb=" O   VAL H 179 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 194 through 195
    Processing sheet with id=AA9, first strand: chain 'D' and resid 36 through 38
      removed outlier: 3.942A  pdb=" N   ALA D  45 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 53
    Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 105
      removed outlier: 3.689A  pdb=" N   HIS D 103 " --> pdb=" O   ASN D 112 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 198 through 202
      removed outlier: 3.814A  pdb=" N   GLN D 199 " --> pdb=" O   THR D 182 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   THR D 182 " --> pdb=" O   GLN D 199 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE D 172 " --> pdb=" O   TRP D 175 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   TYR D 161 " --> pdb=" O   ASN D 149 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLY D 140 " --> pdb=" O   ALA D 658 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   ALA D 658 " --> pdb=" O   GLY D 140 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU D 142 " --> pdb=" O   VAL D 656 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR D 144 " --> pdb=" O   GLY D 654 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLY D 654 " --> pdb=" O   TYR D 144 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TYR D 650 " --> pdb=" O   GLY D 148 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 175 through 185
      removed outlier: 3.698A  pdb=" N   ARG D 178 " --> pdb=" O   TRP D 204 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   TRP D 204 " --> pdb=" O   ARG D 178 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA D 239 " --> pdb=" O   ARG D 215 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ARG D 234 " --> pdb=" O   GLU D 337 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   TYR D 331 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLY D 336 " --> pdb=" O   PHE D 350 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE D 350 " --> pdb=" O   GLY D 336 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLY D 367 " --> pdb=" O   LEU D 355 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TRP D 363 " --> pdb=" O   LEU D 359 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY D 368 " --> pdb=" O   ASN D 379 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA D 377 " --> pdb=" O   GLN D 370 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 376 through 387
      removed outlier: 3.779A  pdb=" N   MET D 386 " --> pdb=" O   GLY D 390 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   GLY D 390 " --> pdb=" O   MET D 386 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASN D 419 " --> pdb=" O   ALA D 391 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER D 393 " --> pdb=" O   LEU D 417 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU D 417 " --> pdb=" O   SER D 393 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ASP D 395 " --> pdb=" O   ARG D 415 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG D 415 " --> pdb=" O   ASP D 395 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   GLY D 411 " --> pdb=" O   ALA D 399 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL D 432 " --> pdb=" O   TYR D 418 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ILE D 429 " --> pdb=" O   THR D 489 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   THR D 489 " --> pdb=" O   ILE D 429 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   LEU D 431 " --> pdb=" O   THR D 487 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   THR D 487 " --> pdb=" O   LEU D 431 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY D 433 " --> pdb=" O   GLN D 485 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ARG D 481 " --> pdb=" O   SER D 437 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLN D 516 " --> pdb=" O   SER D 503 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 529 through 537
      removed outlier: 3.620A  pdb=" N   ALA D 550 " --> pdb=" O   SER D 533 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   MET D 578 " --> pdb=" O   LEU D 551 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ALA D 572 " --> pdb=" O   PHE D 557 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR D 610 " --> pdb=" O   ASN D 588 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL D 606 " --> pdb=" O   VAL D 592 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLY D 594 " --> pdb=" O   TYR D 604 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   TYR D 604 " --> pdb=" O   GLY D 594 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASN D 634 " --> pdb=" O   SER D 653 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASN D 636 " --> pdb=" O   GLY D 651 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY D 651 " --> pdb=" O   ASN D 636 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN D 647 " --> pdb=" O   SER D 640 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY D 655 " --> pdb=" O   GLY D 666 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY D 666 " --> pdb=" O   GLY D 655 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 256 through 260
      removed outlier: 4.062A  pdb=" N   ILE D 256 " --> pdb=" O   ILE D 287 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE D 287 " --> pdb=" O   ILE D 256 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY D 258 " --> pdb=" O   PHE D 285 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 273 through 280
      removed outlier: 6.713A  pdb=" N   ILE D 268 " --> pdb=" O   ILE D 275 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   ASN D 277 " --> pdb=" O   VAL D 266 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   VAL D 266 " --> pdb=" O   ASN D 277 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   THR D 279 " --> pdb=" O   ALA D 264 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   ALA D 264 " --> pdb=" O   THR D 279 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR D 267 " --> pdb=" O   THR D 302 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   THR D 302 " --> pdb=" O   THR D 267 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL D 301 " --> pdb=" O   PHE D 313 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE D 313 " --> pdb=" O   VAL D 301 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 402 through 403
      removed outlier: 3.540A  pdb=" N   LEU D 403 " --> pdb=" O   SER D 407 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   SER D 407 " --> pdb=" O   LEU D 403 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'D' and resid 699 through 701
    Processing sheet with id=AC2, first strand: chain 'D' and resid 751 through 756
      removed outlier: 3.623A  pdb=" N   ILE D 751 " --> pdb=" O   MET D 792 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   LEU D 753 " --> pdb=" O   SER D 790 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   SER D 790 " --> pdb=" O   LEU D 753 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   MET D 755 " --> pdb=" O   TYR D 788 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   TYR D 788 " --> pdb=" O   MET D 755 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLN D 786 " --> pdb=" O   ALA D 782 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   TYR D 788 " --> pdb=" O   ILE D 780 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ILE D 780 " --> pdb=" O   TYR D 788 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   SER D 790 " --> pdb=" O   SER D 778 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   SER D 778 " --> pdb=" O   SER D 790 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL D 770 " --> pdb=" O   GLY D 779 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   MET D 769 " --> pdb=" O   LYS D 801 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   CYS D 810 " --> pdb=" O   VAL D 800 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 25 through 30
      removed outlier: 3.701A  pdb=" N   ARG F   8 " --> pdb=" O   VAL G  25 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   TYR F  10 " --> pdb=" O   LEU G  27 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ASP G  29 " --> pdb=" O   TYR F  10 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER F   3 " --> pdb=" O   ILE G 139 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE F   5 " --> pdb=" O   ILE G 137 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE G 137 " --> pdb=" O   ILE F   5 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA G 135 " --> pdb=" O   ILE F   7 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER G 144 " --> pdb=" O   ARG G  60 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   ARG G  60 " --> pdb=" O   SER G 144 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL G  61 " --> pdb=" O   VAL G 104 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL G 104 " --> pdb=" O   VAL G  61 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 18 through 19
      removed outlier: 3.784A  pdb=" N   ALA F 129 " --> pdb=" O   VAL F  47 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 62 through 63
    Processing sheet with id=AC6, first strand: chain 'F' and resid 67 through 68
      removed outlier: 3.631A  pdb=" N   ILE C 108 " --> pdb=" O   PHE F 149 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   VAL C   9 " --> pdb=" O   TYR C 114 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'F' and resid 67 through 68
      removed outlier: 3.631A  pdb=" N   ILE C 108 " --> pdb=" O   PHE F 149 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE C 107 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL C  87 " --> pdb=" O   SER C 109 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TRP C  84 " --> pdb=" O   GLU C  38 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASN C  86 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TRP C  36 " --> pdb=" O   ASN C  86 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   PHE C  55 " --> pdb=" O   ILE C  33 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'G' and resid 17 through 18
      removed outlier: 3.799A  pdb=" N   THR G  17 " --> pdb=" O   THR G  52 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   THR G  52 " --> pdb=" O   THR G  17 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'G' and resid 46 through 47
      removed outlier: 3.822A  pdb=" N   GLN G 118 " --> pdb=" O   GLN G  89 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLN G  89 " --> pdb=" O   GLN G 118 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 2 through 3
      removed outlier: 3.673A  pdb=" N   GLU C  18 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE C  67 " --> pdb=" O   GLU C  18 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ARG C  66 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 132 through 135
      removed outlier: 3.505A  pdb=" N   LEU C 142 " --> pdb=" O   SER C 173 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER C 173 " --> pdb=" O   LEU C 142 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 165 through 167
      removed outlier: 4.079A  pdb=" N   ALA C 165 " --> pdb=" O   VAL C 152 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   VAL C 152 " --> pdb=" O   ALA C 165 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   VAL C 167 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   LEU C 150 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   GLU C 154 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   ARG C 188 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)

    307 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.51

  Time building geometry restraints manager: 3.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4015
        1.35 -     1.47: 2946
        1.47 -     1.59: 5215
        1.59 -     1.71: 0
        1.71 -     1.83: 62
  Bond restraints: 12238
  Sorted by residual:
  bond pdb=" C   ILE D 210 "
       pdb=" N   PRO D 211 "
    ideal  model  delta    sigma   weight residual
    1.336  1.376 -0.040 1.20e-02 6.94e+03 1.13e+01
  bond pdb=" C   PRO D  29 "
       pdb=" N   PRO D  30 "
    ideal  model  delta    sigma   weight residual
    1.334  1.369 -0.035 1.11e-02 8.12e+03 9.95e+00
  bond pdb=" CB  PRO F 137 "
       pdb=" CG  PRO F 137 "
    ideal  model  delta    sigma   weight residual
    1.492  1.358  0.134 5.00e-02 4.00e+02 7.23e+00
  bond pdb=" CB  PRO F  55 "
       pdb=" CG  PRO F  55 "
    ideal  model  delta    sigma   weight residual
    1.492  1.380  0.112 5.00e-02 4.00e+02 5.04e+00
  bond pdb=" N   PRO H  85 "
       pdb=" CA  PRO H  85 "
    ideal  model  delta    sigma   weight residual
    1.469  1.442  0.027 1.28e-02 6.10e+03 4.41e+00
  ... (remaining 12233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.73: 16674
        7.73 -    15.46: 22
       15.46 -    23.19: 2
       23.19 -    30.92: 4
       30.92 -    38.66: 4
  Bond angle restraints: 16706
  Sorted by residual:
  angle pdb=" C   THR C  51 "
        pdb=" N   PRO C  52 "
        pdb=" CA  PRO C  52 "
      ideal   model   delta    sigma   weight residual
     120.38  153.72  -33.34 1.03e+00 9.43e-01 1.05e+03
  angle pdb=" C   VAL F 136 "
        pdb=" N   PRO F 137 "
        pdb=" CA  PRO F 137 "
      ideal   model   delta    sigma   weight residual
     119.84  158.50  -38.66 1.25e+00 6.40e-01 9.56e+02
  angle pdb=" C   SER F  54 "
        pdb=" N   PRO F  55 "
        pdb=" CA  PRO F  55 "
      ideal   model   delta    sigma   weight residual
     119.84  158.04  -38.20 1.25e+00 6.40e-01 9.34e+02
  angle pdb=" C   PHE H  84 "
        pdb=" N   PRO H  85 "
        pdb=" CA  PRO H  85 "
      ideal   model   delta    sigma   weight residual
     119.84  154.63  -34.79 1.25e+00 6.40e-01 7.75e+02
  angle pdb=" C   LYS F  35 "
        pdb=" N   GLN F  36 "
        pdb=" CA  GLN F  36 "
      ideal   model   delta    sigma   weight residual
     121.54  141.44  -19.90 1.91e+00 2.74e-01 1.09e+02
  ... (remaining 16701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.92: 7142
       26.92 -    53.84: 77
       53.84 -    80.77: 12
       80.77 -   107.69: 2
      107.69 -   134.61: 3
  Dihedral angle restraints: 7236
    sinusoidal: 2694
      harmonic: 4542
  Sorted by residual:
  dihedral pdb=" CA  PRO D  30 "
           pdb=" C   PRO D  30 "
           pdb=" N   GLY D  31 "
           pdb=" CA  GLY D  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   45.39  134.61     0      5.00e+00 4.00e-02 7.25e+02
  dihedral pdb=" CA  LYS F  35 "
           pdb=" C   LYS F  35 "
           pdb=" N   GLN F  36 "
           pdb=" CA  GLN F  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   55.61  124.39     0      5.00e+00 4.00e-02 6.19e+02
  dihedral pdb=" CA  TYR H 175 "
           pdb=" C   TYR H 175 "
           pdb=" N   PRO H 176 "
           pdb=" CA  PRO H 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   56.60  123.40     0      5.00e+00 4.00e-02 6.09e+02
  ... (remaining 7233 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1526
       0.065 -    0.130: 312
       0.130 -    0.195: 57
       0.195 -    0.261: 13
       0.261 -    0.326: 4
  Chirality restraints: 1912
  Sorted by residual:
  chirality pdb=" CB  ILE D 382 "
            pdb=" CA  ILE D 382 "
            pdb=" CG1 ILE D 382 "
            pdb=" CG2 ILE D 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.65e+00
  chirality pdb=" CA  VAL F 136 "
            pdb=" N   VAL F 136 "
            pdb=" C   VAL F 136 "
            pdb=" CB  VAL F 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.76   -0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  ASP D 722 "
            pdb=" N   ASP D 722 "
            pdb=" C   ASP D 722 "
            pdb=" CB  ASP D 722 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 1909 not shown)

  Planarity restraints: 2200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR H 175 "    0.037 2.00e-02 2.50e+03   7.37e-02 5.42e+01
        pdb=" C   TYR H 175 "   -0.127 2.00e-02 2.50e+03
        pdb=" O   TYR H 175 "    0.046 2.00e-02 2.50e+03
        pdb=" N   PRO H 176 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D  30 "   -0.034 2.00e-02 2.50e+03   6.87e-02 4.72e+01
        pdb=" C   PRO D  30 "    0.119 2.00e-02 2.50e+03
        pdb=" O   PRO D  30 "   -0.045 2.00e-02 2.50e+03
        pdb=" N   GLY D  31 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  35 "   -0.031 2.00e-02 2.50e+03   6.01e-02 3.61e+01
        pdb=" C   LYS F  35 "    0.104 2.00e-02 2.50e+03
        pdb=" O   LYS F  35 "   -0.038 2.00e-02 2.50e+03
        pdb=" N   GLN F  36 "   -0.035 2.00e-02 2.50e+03
  ... (remaining 2197 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.86: 3866
        2.86 -     3.37: 8561
        3.37 -     3.88: 18589
        3.88 -     4.39: 17536
        4.39 -     4.90: 32878
  Nonbonded interactions: 81430
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 564 "
            pdb=" OG  SER D 567 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O   THR G  62 "
            pdb=" OG1 THR G 142 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   LEU C 122 "
            pdb=" OH  TYR C 148 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" OG1 THR H 201 "
            pdb=" OD1 ASP H 203 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   THR H 210 "
            pdb=" OG  SER H 270 "
     model   vdw
     2.369 3.040
  ... (remaining 81425 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=0.50 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.110
  Process input model:                     32.540
  Find NCS groups from input model:        0.130
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.134  12244  Z= 0.318
  Angle     :  1.370  38.655  16718  Z= 0.864
  Chirality :  0.058   0.326   1912
  Planarity :  0.008   0.074   2200
  Dihedral  :  9.492 134.608   4330
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.64 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.87 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.94 %
    Twisted General : 0.20 %

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: -3.72 (0.18), residues: 1572
  helix: -5.35 (0.25), residues: 18
  sheet: -1.76 (0.21), residues: 546
  loop : -2.99 (0.15), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP H 103 
 HIS   0.010   0.002   HIS D 409 
 PHE   0.027   0.003   PHE C  55 
 TYR   0.022   0.002   TYR H  64 
 ARG   0.006   0.001   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30399 (  303)
  hydrogen bonds       : angle      11.82697 (  834)
  SS BOND              : bond        0.00628 (    6)
  SS BOND              : angle       1.69401 (   12)
  covalent geometry    : bond        0.00649 (12238)
  covalent geometry    : angle       1.36993 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 379
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   64 TYR cc_start: 0.6248 (m-80) cc_final: 0.6028 (m-80)
REVERT: H   84 PHE cc_start: 0.6407 (t80) cc_final: 0.5664 (t80)
REVERT: H  102 PRO cc_start: 0.6520 (Cg_exo) cc_final: 0.6186 (Cg_endo)
REVERT: H  107 LEU cc_start: 0.8538 (mt) cc_final: 0.8172 (mt)
REVERT: H  130 ILE cc_start: 0.8040 (mt) cc_final: 0.7775 (mt)
REVERT: H  206 ASN cc_start: 0.7807 (m-40) cc_final: 0.7159 (m-40)
REVERT: D  151 VAL cc_start: 0.7672 (t) cc_final: 0.7367 (t)
REVERT: D  208 ASP cc_start: 0.5946 (p0) cc_final: 0.5483 (m-30)
REVERT: D  303 ILE cc_start: 0.7400 (mt) cc_final: 0.7033 (tt)
REVERT: D  346 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7381 (mp0)
REVERT: D  481 ARG cc_start: 0.7081 (ttt180) cc_final: 0.6439 (ttt90)
REVERT: D  708 TYR cc_start: 0.7324 (m-80) cc_final: 0.6923 (m-10)
REVERT: D  725 ASP cc_start: 0.7690 (t0) cc_final: 0.7192 (m-30)
REVERT: D  769 MET cc_start: 0.6481 (mmm) cc_final: 0.6207 (tmm)
REVERT: D  793 PRO cc_start: 0.6131 (Cg_endo) cc_final: 0.5156 (Cg_exo)
REVERT: F    4 THR cc_start: 0.7803 (p) cc_final: 0.7568 (p)
REVERT: F    6 THR cc_start: 0.7855 (m) cc_final: 0.7567 (t)
REVERT: F   16 CYS cc_start: 0.8144 (m) cc_final: 0.7711 (m)
REVERT: F   79 LEU cc_start: 0.8468 (tp) cc_final: 0.8239 (tt)
REVERT: F  116 THR cc_start: 0.7867 (p) cc_final: 0.7586 (t)
REVERT: G   24 THR cc_start: 0.7937 (m) cc_final: 0.7664 (p)
REVERT: C   72 ASN cc_start: 0.8665 (m110) cc_final: 0.8457 (t0)
REVERT: C  104 GLN cc_start: 0.7678 (mt0) cc_final: 0.7453 (mt0)
REVERT: C  160 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7274 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 380
  average time/residue: 0.2577
  time to fit residues: 138.1141
Evaluate side-chains
  213 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    5.9990
   chunk 118 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 122 optimal weight:    0.0170
   chunk 47 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 141 optimal weight:    1.9990
   overall best weight:    2.2024

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

Flipped N/Q/H residues before XYZ refinement:
H  45 HIS
H  59 GLN
H 279 GLN
** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 328 HIS
D 344 GLN
D 370 GLN
D 580 HIS
D 661 ASN
D 718 ASN
F  77 ASN
G  78 GLN
G  82 GLN
G 114 HIS
C 101 ASN
C 164 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.177713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152059 restraints weight = 16683.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.148873 restraints weight = 32664.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.147748 restraints weight = 35976.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12244  Z= 0.208
  Angle     :  0.741  10.364  16718  Z= 0.390
  Chirality :  0.047   0.239   1912
  Planarity :  0.007   0.112   2200
  Dihedral  :  5.689  59.861   1719
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.15 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 10.73 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.33 %
    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: -2.78 (0.19), residues: 1572
  helix: -4.65 (0.60), residues: 24
  sheet: -0.90 (0.22), residues: 565
  loop : -2.49 (0.16), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 198 
 HIS   0.008   0.001   HIS D 200 
 PHE   0.021   0.003   PHE D 525 
 TYR   0.020   0.002   TYR F  10 
 ARG   0.010   0.001   ARG C 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05355 (  303)
  hydrogen bonds       : angle       7.00324 (  834)
  SS BOND              : bond        0.00563 (    6)
  SS BOND              : angle       1.16335 (   12)
  covalent geometry    : bond        0.00459 (12238)
  covalent geometry    : angle       0.74047 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 250
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  187 CYS cc_start: 0.5048 (OUTLIER) cc_final: 0.4659 (p)
REVERT: D   82 MET cc_start: 0.4506 (tmm) cc_final: 0.4036 (tmm)
REVERT: D   96 MET cc_start: 0.4298 (mtp) cc_final: 0.3086 (ttt)
REVERT: D  125 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.8020 (ttp80)
REVERT: D  207 ARG cc_start: 0.7942 (ttt90) cc_final: 0.7460 (tpt-90)
REVERT: D  291 TYR cc_start: 0.7858 (m-80) cc_final: 0.7325 (m-80)
REVERT: D  396 MET cc_start: 0.7461 (tmm) cc_final: 0.7012 (tmm)
REVERT: D  397 THR cc_start: 0.8414 (m) cc_final: 0.7524 (p)
REVERT: D  413 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8584 (m)
REVERT: D  452 MET cc_start: 0.5484 (OUTLIER) cc_final: 0.5062 (ptp)
REVERT: D  481 ARG cc_start: 0.7982 (ttt180) cc_final: 0.7514 (ttt90)
REVERT: D  487 THR cc_start: 0.7804 (p) cc_final: 0.7595 (m)
REVERT: D  653 SER cc_start: 0.8762 (p) cc_final: 0.8536 (t)
REVERT: D  792 MET cc_start: 0.6567 (mmm) cc_final: 0.6220 (tmm)
REVERT: D  814 TYR cc_start: 0.7624 (p90) cc_final: 0.7344 (p90)
REVERT: F   77 ASN cc_start: 0.6166 (OUTLIER) cc_final: 0.5248 (m-40)
REVERT: F   81 LEU cc_start: 0.6500 (mm) cc_final: 0.6153 (tp)
REVERT: G   14 LYS cc_start: 0.8508 (mmpt) cc_final: 0.8036 (mtmt)
REVERT: G   24 THR cc_start: 0.8203 (m) cc_final: 0.7789 (p)
REVERT: G  103 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8671 (p)
REVERT: C  126 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6860 (pp30)
REVERT: C  130 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7563 (mmtm)
REVERT: C  204 MET cc_start: 0.1126 (mmp) cc_final: -0.2508 (ptm)
  outliers start: 39
  outliers final: 22
  residues processed: 279
  average time/residue: 0.2518
  time to fit residues: 101.1126
Evaluate side-chains
  223 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  275 THR
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  248 SER
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  413 SER
Chi-restraints excluded: chain D residue  452 MET
Chi-restraints excluded: chain D residue  523 THR
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  650 TYR
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   77 ASN
Chi-restraints excluded: chain F residue   95 LEU
Chi-restraints excluded: chain G residue   56 VAL
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue  103 THR
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  112 LYS
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 150 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 143 optimal weight:   10.0000
   chunk 107 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 152 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 104 optimal weight:    8.9990
   chunk 37 optimal weight:    0.2980
   chunk 145 optimal weight:    0.5980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
H  46 ASN
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 103 HIS
D 112 ASN
D 295 ASN
D 328 HIS
G 114 HIS
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.173258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.156457 restraints weight = 27302.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147578 restraints weight = 50732.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.144499 restraints weight = 31927.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.5452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12244  Z= 0.145
  Angle     :  0.632   9.289  16718  Z= 0.327
  Chirality :  0.045   0.203   1912
  Planarity :  0.006   0.111   2200
  Dihedral  :  5.077  60.238   1719
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.13 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 13.92 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.19), residues: 1572
  helix: -4.87 (0.64), residues: 18
  sheet: -0.58 (0.22), residues: 579
  loop : -2.36 (0.17), residues: 975

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 530 
 HIS   0.014   0.001   HIS D 328 
 PHE   0.020   0.002   PHE D 146 
 TYR   0.014   0.001   TYR D 144 
 ARG   0.007   0.000   ARG C 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04313 (  303)
  hydrogen bonds       : angle       6.40101 (  834)
  SS BOND              : bond        0.00490 (    6)
  SS BOND              : angle       1.22240 (   12)
  covalent geometry    : bond        0.00328 (12238)
  covalent geometry    : angle       0.63152 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 212
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  187 CYS cc_start: 0.4829 (OUTLIER) cc_final: 0.4230 (p)
REVERT: D   12 ASP cc_start: 0.6998 (p0) cc_final: 0.6549 (t0)
REVERT: D   82 MET cc_start: 0.4427 (tmm) cc_final: 0.4091 (tmm)
REVERT: D  291 TYR cc_start: 0.7889 (m-80) cc_final: 0.7493 (m-80)
REVERT: D  397 THR cc_start: 0.8487 (m) cc_final: 0.8247 (m)
REVERT: D  481 ARG cc_start: 0.8003 (ttt180) cc_final: 0.7466 (ttt90)
REVERT: D  792 MET cc_start: 0.7033 (mmm) cc_final: 0.6704 (tmm)
REVERT: F   81 LEU cc_start: 0.6523 (mm) cc_final: 0.6222 (tp)
REVERT: G   14 LYS cc_start: 0.8738 (mmpt) cc_final: 0.8092 (mtmt)
REVERT: C   16 LYS cc_start: 0.8911 (tptt) cc_final: 0.8420 (ttpp)
REVERT: C  126 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7269 (pp30)
REVERT: C  204 MET cc_start: 0.1510 (mmp) cc_final: 0.1266 (mmm)
  outliers start: 45
  outliers final: 32
  residues processed: 246
  average time/residue: 0.2261
  time to fit residues: 81.5117
Evaluate side-chains
  216 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 182
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   46 ASN
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  138 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  575 SER
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  650 TYR
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain F residue   16 CYS
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   77 ASN
Chi-restraints excluded: chain F residue   95 LEU
Chi-restraints excluded: chain F residue   97 ASN
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain G residue   18 VAL
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue  133 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  112 LYS
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 138 optimal weight:    8.9990
   chunk 121 optimal weight:    6.9990
   chunk 29 optimal weight:    0.3980
   chunk 63 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 106 optimal weight:    0.0670
   chunk 146 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 119 optimal weight:    4.9990
   chunk 149 optimal weight:   10.0000
   overall best weight:    1.6924

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

Flipped N/Q/H residues before XYZ refinement:
H  33 ASN
H  46 ASN
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 490 GLN
** D 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 142 HIS
G 114 HIS
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.170562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.147996 restraints weight = 17084.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.146232 restraints weight = 39457.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.140368 restraints weight = 39133.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.6171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12244  Z= 0.150
  Angle     :  0.624   8.526  16718  Z= 0.323
  Chirality :  0.045   0.213   1912
  Planarity :  0.006   0.109   2200
  Dihedral  :  4.878  55.083   1719
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 14.00 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.19), residues: 1572
  helix: -4.98 (0.47), residues: 25
  sheet: -0.32 (0.22), residues: 583
  loop : -2.33 (0.17), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 802 
 HIS   0.018   0.001   HIS H  45 
 PHE   0.023   0.002   PHE D 525 
 TYR   0.016   0.001   TYR D 436 
 ARG   0.005   0.001   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04122 (  303)
  hydrogen bonds       : angle       6.04598 (  834)
  SS BOND              : bond        0.00267 (    6)
  SS BOND              : angle       1.20207 (   12)
  covalent geometry    : bond        0.00342 (12238)
  covalent geometry    : angle       0.62311 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 208
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   12 ASP cc_start: 0.7071 (p0) cc_final: 0.6569 (t0)
REVERT: D  237 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7718 (tt0)
REVERT: D  333 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8301 (mp)
REVERT: D  396 MET cc_start: 0.7283 (tmm) cc_final: 0.6745 (tmm)
REVERT: D  481 ARG cc_start: 0.7772 (ttt180) cc_final: 0.7311 (ttt90)
REVERT: D  799 GLN cc_start: 0.7893 (mp10) cc_final: 0.7578 (tm-30)
REVERT: F   99 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7286 (mp10)
REVERT: G   14 LYS cc_start: 0.8609 (mmpt) cc_final: 0.8051 (mtmt)
REVERT: G  141 TYR cc_start: 0.8746 (m-80) cc_final: 0.8263 (m-80)
REVERT: C   16 LYS cc_start: 0.8899 (tptt) cc_final: 0.8494 (ttpp)
REVERT: C  100 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7471 (mm-30)
  outliers start: 56
  outliers final: 37
  residues processed: 247
  average time/residue: 0.2244
  time to fit residues: 82.2562
Evaluate side-chains
  227 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 188
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   46 ASN
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  130 ILE
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain H residue  214 SER
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  138 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  575 SER
Chi-restraints excluded: chain D residue  589 LEU
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain F residue   16 CYS
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   97 ASN
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain G residue   18 VAL
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   36 MET
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  133 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  112 LYS
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 121 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 146 optimal weight:    1.9990
   chunk 3 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0470
   chunk 120 optimal weight:    2.9990
   chunk 147 optimal weight:    5.9990
   overall best weight:    2.2086

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

Flipped N/Q/H residues before XYZ refinement:
H  32 GLN
H  46 ASN
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 512 ASN
** D 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  94 GLN
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.177936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.162704 restraints weight = 15987.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.160658 restraints weight = 34579.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.159554 restraints weight = 39945.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3801
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3801 r_free = 0.3801    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3801 r_free = 0.3801    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3801
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.6798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12244  Z= 0.176
  Angle     :  0.654   8.329  16718  Z= 0.337
  Chirality :  0.045   0.199   1912
  Planarity :  0.006   0.129   2200
  Dihedral  :  5.089  60.251   1719
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 15.24 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.19), residues: 1572
  helix: -4.73 (0.42), residues: 37
  sheet: -0.19 (0.22), residues: 561
  loop : -2.33 (0.17), residues: 974

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 802 
 HIS   0.009   0.001   HIS H  45 
 PHE   0.017   0.002   PHE G  33 
 TYR   0.022   0.002   TYR D 436 
 ARG   0.006   0.001   ARG C  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 (  303)
  hydrogen bonds       : angle       5.96916 (  834)
  SS BOND              : bond        0.00335 (    6)
  SS BOND              : angle       0.97047 (   12)
  covalent geometry    : bond        0.00405 (12238)
  covalent geometry    : angle       0.65369 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 189
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  237 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7909 (tt0)
REVERT: D  333 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8319 (mp)
REVERT: D  379 ASN cc_start: 0.8090 (t0) cc_final: 0.7847 (t0)
REVERT: D  396 MET cc_start: 0.7281 (tmm) cc_final: 0.6628 (tmm)
REVERT: D  481 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7273 (ttt90)
REVERT: F   17 SER cc_start: 0.8906 (t) cc_final: 0.8360 (p)
REVERT: G   14 LYS cc_start: 0.8708 (mmpt) cc_final: 0.8167 (mttt)
REVERT: G   78 GLN cc_start: 0.7585 (mt0) cc_final: 0.7338 (mt0)
REVERT: G  141 TYR cc_start: 0.8810 (m-80) cc_final: 0.8368 (m-80)
REVERT: C   16 LYS cc_start: 0.8900 (tptt) cc_final: 0.8542 (ttpp)
REVERT: C  204 MET cc_start: 0.1130 (mmm) cc_final: -0.0321 (mmm)
  outliers start: 51
  outliers final: 41
  residues processed: 227
  average time/residue: 0.2100
  time to fit residues: 71.8189
Evaluate side-chains
  218 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   46 ASN
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  130 ILE
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  193 LEU
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain H residue  214 SER
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  518 GLN
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  575 SER
Chi-restraints excluded: chain D residue  589 LEU
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain F residue   16 CYS
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   97 ASN
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain G residue   18 VAL
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   36 MET
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  133 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  112 LYS
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 50 optimal weight:    0.1980
   chunk 94 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 119 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
H  46 ASN
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 809 HIS
F  36 GLN
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.177319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.163020 restraints weight = 16262.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.160770 restraints weight = 31580.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.159416 restraints weight = 39734.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3723 r_free = 0.3723    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3723 r_free = 0.3723    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.7060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12244  Z= 0.138
  Angle     :  0.613  10.088  16718  Z= 0.314
  Chirality :  0.044   0.192   1912
  Planarity :  0.005   0.122   2200
  Dihedral  :  4.836  55.138   1719
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 15.79 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.20), residues: 1572
  helix: -4.59 (0.49), residues: 36
  sheet: -0.14 (0.22), residues: 563
  loop : -2.25 (0.17), residues: 973

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 198 
 HIS   0.009   0.001   HIS H  45 
 PHE   0.028   0.002   PHE D 525 
 TYR   0.023   0.001   TYR D 436 
 ARG   0.004   0.000   ARG C 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03887 (  303)
  hydrogen bonds       : angle       5.75799 (  834)
  SS BOND              : bond        0.00219 (    6)
  SS BOND              : angle       0.94952 (   12)
  covalent geometry    : bond        0.00317 (12238)
  covalent geometry    : angle       0.61282 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 189
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   12 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6495 (t0)
REVERT: D   44 MET cc_start: 0.6734 (ttt) cc_final: 0.6330 (ttp)
REVERT: D  234 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6801 (ttm-80)
REVERT: D  237 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7903 (tt0)
REVERT: D  333 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8246 (mp)
REVERT: D  481 ARG cc_start: 0.7965 (ttt180) cc_final: 0.7225 (ttt90)
REVERT: F   17 SER cc_start: 0.8901 (t) cc_final: 0.8266 (p)
REVERT: G   14 LYS cc_start: 0.8736 (mmpt) cc_final: 0.8158 (mtmt)
REVERT: G  141 TYR cc_start: 0.8822 (m-80) cc_final: 0.8442 (m-80)
REVERT: C   16 LYS cc_start: 0.8914 (tptt) cc_final: 0.8506 (ttpp)
REVERT: C  204 MET cc_start: 0.1167 (mmm) cc_final: 0.0365 (mmm)
  outliers start: 54
  outliers final: 40
  residues processed: 229
  average time/residue: 0.2133
  time to fit residues: 73.5118
Evaluate side-chains
  220 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 176
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  130 ILE
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain H residue  214 SER
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  492 LEU
Chi-restraints excluded: chain D residue  518 GLN
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  575 SER
Chi-restraints excluded: chain D residue  589 LEU
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain F residue   16 CYS
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain G residue   18 VAL
Chi-restraints excluded: chain G residue   36 MET
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  133 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  112 LYS
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 105 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 85 optimal weight:    9.9990
   chunk 112 optimal weight:    0.0970
   chunk 71 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    8.9990
   chunk 79 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   overall best weight:    2.1382

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

Flipped N/Q/H residues before XYZ refinement:
H  46 ASN
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 262 GLN
D 324 GLN
G  78 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.174935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.163182 restraints weight = 25213.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.153692 restraints weight = 49078.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.148403 restraints weight = 31599.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3479
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.7392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12244  Z= 0.168
  Angle     :  0.654  12.832  16718  Z= 0.334
  Chirality :  0.045   0.175   1912
  Planarity :  0.005   0.124   2200
  Dihedral  :  5.010  53.495   1719
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 16.49 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.19), residues: 1572
  helix: -4.42 (0.50), residues: 37
  sheet: -0.22 (0.22), residues: 568
  loop : -2.31 (0.17), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 198 
 HIS   0.003   0.001   HIS D 559 
 PHE   0.029   0.002   PHE D 766 
 TYR   0.025   0.002   TYR D 436 
 ARG   0.005   0.000   ARG C 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04388 (  303)
  hydrogen bonds       : angle       5.82290 (  834)
  SS BOND              : bond        0.00275 (    6)
  SS BOND              : angle       0.76911 (   12)
  covalent geometry    : bond        0.00388 (12238)
  covalent geometry    : angle       0.65358 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 189
  time to evaluate  : 1.202 
Fit side-chains
REVERT: D   12 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6501 (t0)
REVERT: D  138 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8237 (p0)
REVERT: D  237 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7786 (tt0)
REVERT: D  333 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8226 (mp)
REVERT: D  481 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7229 (ttt90)
REVERT: G   14 LYS cc_start: 0.8718 (mmpt) cc_final: 0.8013 (mtmt)
REVERT: G   78 GLN cc_start: 0.7763 (mt0) cc_final: 0.7549 (mt0)
REVERT: C   16 LYS cc_start: 0.9059 (tptt) cc_final: 0.8545 (ttpp)
REVERT: C  204 MET cc_start: 0.2216 (mmm) cc_final: 0.0842 (mmm)
  outliers start: 54
  outliers final: 42
  residues processed: 230
  average time/residue: 0.2014
  time to fit residues: 69.8553
Evaluate side-chains
  224 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 178
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  130 ILE
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain H residue  214 SER
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  138 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  492 LEU
Chi-restraints excluded: chain D residue  518 GLN
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  575 SER
Chi-restraints excluded: chain D residue  589 LEU
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  673 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain D residue  800 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   95 LEU
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain G residue   18 VAL
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   36 MET
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  129 THR
Chi-restraints excluded: chain G residue  133 ILE
Chi-restraints excluded: chain C residue  112 LYS
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 104 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 117 optimal weight:    0.4980
   chunk 140 optimal weight:    4.9990
   chunk 129 optimal weight:    3.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 192 ASN
D 491 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.172609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.162440 restraints weight = 25292.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.152215 restraints weight = 43020.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.146927 restraints weight = 31938.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.7692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12244  Z= 0.175
  Angle     :  0.656  11.612  16718  Z= 0.337
  Chirality :  0.045   0.182   1912
  Planarity :  0.005   0.119   2200
  Dihedral  :  5.158  53.236   1719
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 17.11 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.19), residues: 1572
  helix: -4.27 (0.58), residues: 36
  sheet: -0.24 (0.22), residues: 564
  loop : -2.31 (0.17), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 198 
 HIS   0.004   0.001   HIS D 200 
 PHE   0.027   0.002   PHE D 766 
 TYR   0.025   0.001   TYR D 436 
 ARG   0.004   0.000   ARG C 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04421 (  303)
  hydrogen bonds       : angle       5.88001 (  834)
  SS BOND              : bond        0.00235 (    6)
  SS BOND              : angle       0.68667 (   12)
  covalent geometry    : bond        0.00404 (12238)
  covalent geometry    : angle       0.65555 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 180
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
REVERT: H  101 LYS cc_start: 0.6840 (pttt) cc_final: 0.5854 (tptt)
REVERT: D   12 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6465 (t0)
REVERT: D   44 MET cc_start: 0.7026 (ttt) cc_final: 0.6721 (ttp)
REVERT: D  138 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8075 (p0)
REVERT: D  237 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7832 (tt0)
REVERT: D  333 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8246 (mp)
REVERT: D  481 ARG cc_start: 0.7876 (ttt180) cc_final: 0.7180 (ttt90)
REVERT: D  814 TYR cc_start: 0.7868 (p90) cc_final: 0.7631 (p90)
REVERT: G   14 LYS cc_start: 0.8727 (mmpt) cc_final: 0.8078 (mtmt)
REVERT: G   78 GLN cc_start: 0.7891 (mt0) cc_final: 0.7634 (mt0)
REVERT: G  144 SER cc_start: 0.7974 (p) cc_final: 0.7557 (t)
REVERT: C   16 LYS cc_start: 0.9003 (tptt) cc_final: 0.8560 (ttpp)
REVERT: C  204 MET cc_start: 0.2238 (mmm) cc_final: 0.1166 (mmm)
  outliers start: 48
  outliers final: 44
  residues processed: 218
  average time/residue: 0.2079
  time to fit residues: 68.0551
Evaluate side-chains
  219 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 171
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  130 ILE
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain H residue  214 SER
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  138 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  492 LEU
Chi-restraints excluded: chain D residue  518 GLN
Chi-restraints excluded: chain D residue  523 THR
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  575 SER
Chi-restraints excluded: chain D residue  589 LEU
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  673 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain D residue  800 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   95 LEU
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain G residue   18 VAL
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   36 MET
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  129 THR
Chi-restraints excluded: chain G residue  133 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  112 LYS
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 122 optimal weight:    0.4980
   chunk 81 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 151 optimal weight:    9.9990
   chunk 71 optimal weight:    0.0470
   chunk 102 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 13 optimal weight:   20.0000
   chunk 77 optimal weight:    2.9990
   chunk 108 optimal weight:    6.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    2.1084

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

Flipped N/Q/H residues before XYZ refinement:
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.172507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.161109 restraints weight = 16293.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.157757 restraints weight = 36208.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.157299 restraints weight = 50773.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3775
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3775 r_free = 0.3775    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3775 r_free = 0.3775    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3775
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.7869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12244  Z= 0.166
  Angle     :  0.661  11.227  16718  Z= 0.339
  Chirality :  0.045   0.164   1912
  Planarity :  0.006   0.134   2200
  Dihedral  :  5.147  56.672   1719
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 17.73 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.20), residues: 1572
  helix: -4.24 (0.63), residues: 30
  sheet: -0.26 (0.22), residues: 565
  loop : -2.26 (0.17), residues: 977

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 198 
 HIS   0.004   0.001   HIS D 200 
 PHE   0.033   0.002   PHE D 525 
 TYR   0.025   0.001   TYR D 436 
 ARG   0.005   0.000   ARG C 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  303)
  hydrogen bonds       : angle       5.85185 (  834)
  SS BOND              : bond        0.00203 (    6)
  SS BOND              : angle       0.66327 (   12)
  covalent geometry    : bond        0.00386 (12238)
  covalent geometry    : angle       0.66088 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 183
  time to evaluate  : 1.241 
Fit side-chains
   revert: symmetry clash
REVERT: H  101 LYS cc_start: 0.5912 (pttt) cc_final: 0.5595 (tptt)
REVERT: D   12 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6333 (t0)
REVERT: D   41 ASN cc_start: 0.7814 (m110) cc_final: 0.7393 (m-40)
REVERT: D   51 PHE cc_start: 0.3714 (m-80) cc_final: 0.3409 (m-10)
REVERT: D  138 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8011 (p0)
REVERT: D  234 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7031 (ttm-80)
REVERT: D  237 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7930 (tt0)
REVERT: D  333 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8247 (mp)
REVERT: G   14 LYS cc_start: 0.8694 (mmpt) cc_final: 0.8120 (mtmt)
REVERT: G  144 SER cc_start: 0.7791 (p) cc_final: 0.7373 (t)
REVERT: C   16 LYS cc_start: 0.9014 (tptt) cc_final: 0.8580 (ttpp)
REVERT: C  204 MET cc_start: 0.1777 (mmm) cc_final: 0.0676 (mmm)
  outliers start: 53
  outliers final: 44
  residues processed: 224
  average time/residue: 0.2114
  time to fit residues: 71.1627
Evaluate side-chains
  220 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 171
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  130 ILE
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  193 LEU
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain H residue  214 SER
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  138 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  492 LEU
Chi-restraints excluded: chain D residue  518 GLN
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  575 SER
Chi-restraints excluded: chain D residue  589 LEU
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  673 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain D residue  800 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   95 LEU
Chi-restraints excluded: chain F residue   97 ASN
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain F residue  142 HIS
Chi-restraints excluded: chain G residue    5 ILE
Chi-restraints excluded: chain G residue   18 VAL
Chi-restraints excluded: chain G residue   36 MET
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  129 THR
Chi-restraints excluded: chain G residue  133 ILE
Chi-restraints excluded: chain C residue  112 LYS
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 47 optimal weight:    0.0870
   chunk 94 optimal weight:    1.9990
   chunk 152 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 134 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9980
   chunk 111 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.0162

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

Flipped N/Q/H residues before XYZ refinement:
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.173815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.163249 restraints weight = 25602.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.152189 restraints weight = 52503.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.147064 restraints weight = 32916.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.7879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12244  Z= 0.118
  Angle     :  0.642  11.286  16718  Z= 0.324
  Chirality :  0.044   0.162   1912
  Planarity :  0.005   0.125   2200
  Dihedral  :  4.912  58.968   1719
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.36 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.20), residues: 1572
  helix: -4.00 (0.72), residues: 24
  sheet: -0.22 (0.22), residues: 578
  loop : -2.10 (0.18), residues: 970

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 508 
 HIS   0.002   0.001   HIS D 200 
 PHE   0.032   0.002   PHE D 525 
 TYR   0.023   0.001   TYR D 436 
 ARG   0.005   0.000   ARG D  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03497 (  303)
  hydrogen bonds       : angle       5.67313 (  834)
  SS BOND              : bond        0.00193 (    6)
  SS BOND              : angle       1.46185 (   12)
  covalent geometry    : bond        0.00272 (12238)
  covalent geometry    : angle       0.64103 (16706)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 184
  time to evaluate  : 1.190 
Fit side-chains
REVERT: H  101 LYS cc_start: 0.6858 (pttt) cc_final: 0.5815 (tptt)
REVERT: D   12 ASP cc_start: 0.7149 (p0) cc_final: 0.6520 (t0)
REVERT: D   41 ASN cc_start: 0.7957 (m110) cc_final: 0.7571 (m-40)
REVERT: D  234 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7130 (ttm-80)
REVERT: D  237 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7920 (tt0)
REVERT: D  333 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8137 (mp)
REVERT: D  481 ARG cc_start: 0.7772 (ttt180) cc_final: 0.7068 (ttt90)
REVERT: G   14 LYS cc_start: 0.8778 (mmpt) cc_final: 0.8157 (mtmt)
REVERT: G  141 TYR cc_start: 0.8763 (m-80) cc_final: 0.8447 (m-80)
REVERT: G  144 SER cc_start: 0.7825 (p) cc_final: 0.7358 (t)
REVERT: C   16 LYS cc_start: 0.9053 (tptt) cc_final: 0.8530 (ttpt)
REVERT: C  204 MET cc_start: 0.2144 (mmm) cc_final: 0.1029 (mmm)
  outliers start: 37
  outliers final: 33
  residues processed: 210
  average time/residue: 0.2093
  time to fit residues: 66.2283
Evaluate side-chains
  213 residues out of total 1299 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 177
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  130 ILE
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  206 ASN
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  208 ASP
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  492 LEU
Chi-restraints excluded: chain D residue  518 GLN
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  551 LEU
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  575 SER
Chi-restraints excluded: chain D residue  589 LEU
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  673 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain D residue  800 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain F residue  142 HIS
Chi-restraints excluded: chain G residue   18 VAL
Chi-restraints excluded: chain G residue   32 SER
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  129 THR
Chi-restraints excluded: chain G residue  133 ILE
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  185 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 137 optimal weight:    4.9990
   chunk 112 optimal weight:    7.9990
   chunk 148 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 93 optimal weight:    5.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.171050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.155479 restraints weight = 16402.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.153330 restraints weight = 38184.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.152661 restraints weight = 39541.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.3656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.8031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12244  Z= 0.169
  Angle     :  0.677  12.216  16718  Z= 0.344
  Chirality :  0.045   0.162   1912
  Planarity :  0.006   0.127   2200
  Dihedral  :  5.122  56.463   1719
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.67 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.20), residues: 1572
  helix: -4.87 (0.33), residues: 18
  sheet: -0.25 (0.21), residues: 584
  loop : -2.14 (0.18), residues: 970

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 198 
 HIS   0.004   0.001   HIS D 200 
 PHE   0.043   0.002   PHE H  84 
 TYR   0.025   0.002   TYR D 436 
 ARG   0.006   0.001   ARG D 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04349 (  303)
  hydrogen bonds       : angle       5.79167 (  834)
  SS BOND              : bond        0.00259 (    6)
  SS BOND              : angle       1.18764 (   12)
  covalent geometry    : bond        0.00394 (12238)
  covalent geometry    : angle       0.67614 (16706)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4075.63 seconds
wall clock time: 71 minutes 17.09 seconds (4277.09 seconds total)