Starting phenix.real_space_refine
on Thu Feb 15 10:37:24 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e14_8953/02_2024/6e14_8953.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e14_8953/02_2024/6e14_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e14_8953/02_2024/6e14_8953.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e14_8953/02_2024/6e14_8953.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e14_8953/02_2024/6e14_8953.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e14_8953/02_2024/6e14_8953.pdb"
  }
  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
    Residue "H ARG   60": "NH1" <-> "NH2"
    Residue "H ARG  258": "NH1" <-> "NH2"
    Residue "D ARG  748": "NH1" <-> "NH2"
    Residue "F ARG    8": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.25, per 1000 atoms: 0.60
  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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.35
  Conformation dependent library (CDL) restraints added in 2.5 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: 1.40
  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: 4.21

  Time building geometry restraints manager: 4.73 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:
       94.24 -   107.09: 429
      107.09 -   119.94: 10182
      119.94 -   132.79: 6065
      132.79 -   145.64: 26
      145.64 -   158.50: 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 2.440
  nonbonded pdb=" O   THR G  62 "
            pdb=" OG1 THR G 142 "
     model   vdw
     2.354 2.440
  nonbonded pdb=" O   LEU C 122 "
            pdb=" OH  TYR C 148 "
     model   vdw
     2.358 2.440
  nonbonded pdb=" OG1 THR H 201 "
            pdb=" OD1 ASP H 203 "
     model   vdw
     2.361 2.440
  nonbonded pdb=" O   THR H 210 "
            pdb=" OG  SER H 270 "
     model   vdw
     2.369 2.440
  ... (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
========== 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:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.930
  Check model and map are aligned:         0.160
  Set scattering table:                    0.110
  Process input model:                     34.910
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.340
-------------------------------------------------------------------------------
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  12238  Z= 0.417
  Angle     :  1.370  38.655  16706  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  :  4.71 %
    Favored  : 95.04 %
  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 

*********************** 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 fitting.
    rotamer outliers: 1
    poor density    : 379
  time to evaluate  : 1.350 
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: 0.2473
  time to fit residues: 130.8668
Evaluate side-chains
  213 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 118 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 141 optimal weight:    2.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
H  59 GLN
H 262 GLN
H 279 GLN
D 295 ASN
D 328 HIS
D 344 GLN
D 370 GLN
** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 580 HIS
D 661 ASN
D 718 ASN
F  77 ASN
** F 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  78 GLN
G  82 GLN
G 105 GLN
C  17 GLN
C 101 ASN
C 164 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.4787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12238  Z= 0.379
  Angle     :  0.786   9.661  16706  Z= 0.418
  Chirality :  0.048   0.264   1912
  Planarity :  0.007   0.114   2200
  Dihedral  :  5.945  62.709   1719
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.28 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 10.81 %
    Favored  : 85.54 %
  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: -2.86 (0.19), residues: 1572
  helix: -5.17 (0.36), residues: 24
  sheet: -0.95 (0.22), residues: 561
  loop : -2.53 (0.16), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 198 
 HIS   0.007   0.001   HIS D 200 
 PHE   0.020   0.003   PHE D 350 
 TYR   0.024   0.002   TYR G  75 
 ARG   0.008   0.001   ARG C 116 

*********************** 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
  300 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 255
  time to evaluate  : 1.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   64 TYR cc_start: 0.6722 (m-80) cc_final: 0.5953 (m-80)
REVERT: H   84 PHE cc_start: 0.5374 (t80) cc_final: 0.4968 (t80)
REVERT: H  187 CYS cc_start: 0.5150 (OUTLIER) cc_final: 0.4504 (p)
REVERT: H  224 GLN cc_start: 0.7841 (tp40) cc_final: 0.7631 (mm110)
REVERT: D  125 ARG cc_start: 0.8767 (ttp-110) cc_final: 0.8108 (ttp80)
REVERT: D  172 ILE cc_start: 0.8675 (mt) cc_final: 0.8467 (mm)
REVERT: D  206 GLU cc_start: 0.8018 (pt0) cc_final: 0.7757 (tt0)
REVERT: D  207 ARG cc_start: 0.7714 (ttt90) cc_final: 0.6545 (tpt-90)
REVERT: D  291 TYR cc_start: 0.7900 (m-80) cc_final: 0.7521 (m-80)
REVERT: D  298 ASP cc_start: 0.7143 (m-30) cc_final: 0.6752 (m-30)
REVERT: D  300 GLN cc_start: 0.6986 (tm-30) cc_final: 0.6583 (tm-30)
REVERT: D  346 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7380 (mp0)
REVERT: D  371 LEU cc_start: 0.8293 (mt) cc_final: 0.7737 (tp)
REVERT: D  379 ASN cc_start: 0.8438 (t0) cc_final: 0.8131 (t0)
REVERT: D  396 MET cc_start: 0.6357 (tmm) cc_final: 0.6089 (tmm)
REVERT: D  397 THR cc_start: 0.8455 (m) cc_final: 0.8252 (m)
REVERT: D  413 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8340 (m)
REVERT: D  452 MET cc_start: 0.4985 (OUTLIER) cc_final: 0.4679 (ptp)
REVERT: D  481 ARG cc_start: 0.7914 (ttt180) cc_final: 0.6938 (ttt90)
REVERT: D  769 MET cc_start: 0.6836 (mmm) cc_final: 0.6275 (tmm)
REVERT: D  792 MET cc_start: 0.7822 (mmm) cc_final: 0.7118 (tmm)
REVERT: D  799 GLN cc_start: 0.7440 (mp10) cc_final: 0.7101 (mp10)
REVERT: D  814 TYR cc_start: 0.7145 (p90) cc_final: 0.6865 (p90)
REVERT: F    6 THR cc_start: 0.8783 (m) cc_final: 0.8412 (p)
REVERT: F   16 CYS cc_start: 0.8089 (m) cc_final: 0.7771 (m)
REVERT: F   77 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.6408 (m-40)
REVERT: F   81 LEU cc_start: 0.7129 (mm) cc_final: 0.6690 (tp)
REVERT: F  116 THR cc_start: 0.7916 (p) cc_final: 0.7637 (t)
REVERT: G   14 LYS cc_start: 0.8438 (mmpt) cc_final: 0.7385 (mtmt)
REVERT: G   46 ASP cc_start: 0.7547 (t70) cc_final: 0.7307 (m-30)
REVERT: G  105 GLN cc_start: 0.7336 (mm110) cc_final: 0.7027 (tp40)
REVERT: C   16 LYS cc_start: 0.8834 (tptt) cc_final: 0.8021 (ttpp)
REVERT: C   23 THR cc_start: 0.8394 (m) cc_final: 0.7960 (p)
REVERT: C   38 GLU cc_start: 0.8536 (tt0) cc_final: 0.7958 (mt-10)
REVERT: C   57 MET cc_start: 0.8249 (mtm) cc_final: 0.7970 (mtp)
REVERT: C  126 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7254 (pp30)
REVERT: C  130 LYS cc_start: 0.8398 (mmtm) cc_final: 0.7894 (mmtm)
REVERT: C  160 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7286 (mmt-90)
REVERT: C  193 TYR cc_start: 0.8603 (m-80) cc_final: 0.8374 (m-80)
REVERT: C  204 MET cc_start: 0.2836 (mmp) cc_final: 0.2546 (mmm)
  outliers start: 45
  outliers final: 26
  residues processed: 288
  average time/residue: 0.2385
  time to fit residues: 97.6453
Evaluate side-chains
  247 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 216
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
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  167 ASP
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  226 ASP
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  409 HIS
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  564 ASP
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 F residue   97 ASN
Chi-restraints excluded: chain G residue   56 VAL
Chi-restraints excluded: chain G residue   91 ASP
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 78 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 117 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 141 optimal weight:    3.9990
   chunk 153 optimal weight:   10.0000
   chunk 126 optimal weight:    2.9990
   chunk 140 optimal weight:    0.6980
   chunk 48 optimal weight:    8.9990
   chunk 113 optimal weight:    0.9980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
H  45 HIS
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 324 GLN
D 328 HIS
D 490 GLN
C  72 ASN
** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.5553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12238  Z= 0.210
  Angle     :  0.617   8.569  16706  Z= 0.321
  Chirality :  0.044   0.206   1912
  Planarity :  0.006   0.099   2200
  Dihedral  :  5.167  59.207   1719
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.64 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 13.92 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.94 %
    Twisted General : 0.13 %

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: -2.56 (0.19), residues: 1572
  helix: -4.99 (0.44), residues: 25
  sheet: -0.65 (0.22), residues: 560
  loop : -2.38 (0.17), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 802 
 HIS   0.009   0.001   HIS D 328 
 PHE   0.022   0.002   PHE D 146 
 TYR   0.017   0.001   TYR D 436 
 ARG   0.005   0.000   ARG C 116 

*********************** 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
  271 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 225
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   58 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.6872 (pp)
REVERT: H   64 TYR cc_start: 0.7043 (m-80) cc_final: 0.6113 (m-80)
REVERT: H  191 GLN cc_start: 0.6478 (tt0) cc_final: 0.5650 (pm20)
REVERT: D   12 ASP cc_start: 0.6505 (p0) cc_final: 0.5926 (t0)
REVERT: D  244 MET cc_start: 0.8536 (mtt) cc_final: 0.8248 (mtp)
REVERT: D  298 ASP cc_start: 0.7215 (m-30) cc_final: 0.6822 (m-30)
REVERT: D  300 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6435 (tm-30)
REVERT: D  346 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7514 (mp0)
REVERT: D  371 LEU cc_start: 0.8397 (mt) cc_final: 0.7761 (tp)
REVERT: D  397 THR cc_start: 0.8488 (m) cc_final: 0.8147 (p)
REVERT: D  413 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8372 (m)
REVERT: D  481 ARG cc_start: 0.7575 (ttt180) cc_final: 0.6679 (ttt90)
REVERT: D  683 ASP cc_start: 0.7480 (t70) cc_final: 0.7136 (t0)
REVERT: D  769 MET cc_start: 0.6878 (mmm) cc_final: 0.6573 (tmm)
REVERT: D  792 MET cc_start: 0.7816 (mmm) cc_final: 0.7004 (tmm)
REVERT: D  799 GLN cc_start: 0.7323 (mp10) cc_final: 0.7087 (mp10)
REVERT: D  814 TYR cc_start: 0.7022 (p90) cc_final: 0.6597 (p90)
REVERT: F    6 THR cc_start: 0.8771 (m) cc_final: 0.8357 (t)
REVERT: F   81 LEU cc_start: 0.7003 (mm) cc_final: 0.6677 (tp)
REVERT: F  116 THR cc_start: 0.7967 (p) cc_final: 0.7660 (t)
REVERT: G   14 LYS cc_start: 0.8477 (mmpt) cc_final: 0.7426 (mtmt)
REVERT: G  105 GLN cc_start: 0.7432 (mm110) cc_final: 0.7061 (mp10)
REVERT: C   16 LYS cc_start: 0.8816 (tptt) cc_final: 0.8018 (ttpp)
REVERT: C   23 THR cc_start: 0.8423 (m) cc_final: 0.8049 (p)
REVERT: C   57 MET cc_start: 0.8183 (mtm) cc_final: 0.7957 (mtp)
REVERT: C   61 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7797 (mtmt)
REVERT: C   74 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8847 (tm-30)
REVERT: C   79 ARG cc_start: 0.7230 (ptp-170) cc_final: 0.6845 (ptp90)
REVERT: C   80 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7719 (mm-30)
REVERT: C  160 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7190 (mmt-90)
  outliers start: 46
  outliers final: 25
  residues processed: 258
  average time/residue: 0.2261
  time to fit residues: 84.8359
Evaluate side-chains
  217 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 190
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   58 LEU
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue  129 LEU
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  201 THR
Chi-restraints excluded: chain H residue  214 SER
Chi-restraints excluded: chain D residue  122 ASN
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  226 ASP
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  413 SER
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  496 SER
Chi-restraints excluded: chain D residue  581 ASP
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain F residue   97 ASN
Chi-restraints excluded: chain F residue  124 THR
Chi-restraints excluded: chain G residue   91 ASP
Chi-restraints excluded: chain G residue  122 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 140 optimal weight:    9.9990
   chunk 106 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 15 optimal weight:    0.2980
   chunk 67 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 142 optimal weight:    1.9990
   chunk 150 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 134 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    2.4588

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

Flipped N/Q/H residues before XYZ refinement:
H 192 ASN
D 243 ASN
D 379 ASN
F 142 HIS
** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 ASN
** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.6503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12238  Z= 0.295
  Angle     :  0.672  11.387  16706  Z= 0.350
  Chirality :  0.045   0.205   1912
  Planarity :  0.006   0.111   2200
  Dihedral  :  5.375  58.104   1719
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 13.69 %
    Favored  : 81.03 %
  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: -2.49 (0.19), residues: 1572
  helix: -4.72 (0.44), residues: 31
  sheet: -0.55 (0.22), residues: 562
  loop : -2.36 (0.17), residues: 979

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 802 
 HIS   0.005   0.001   HIS D 200 
 PHE   0.025   0.002   PHE D 525 
 TYR   0.023   0.002   TYR H 195 
 ARG   0.006   0.001   ARG C 132 

*********************** 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
  275 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 66
    poor density    : 209
  time to evaluate  : 1.336 
Fit side-chains
   revert: symmetry clash
REVERT: H   58 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6461 (pp)
REVERT: H   84 PHE cc_start: 0.4487 (t80) cc_final: 0.4116 (t80)
REVERT: D  206 GLU cc_start: 0.7975 (tt0) cc_final: 0.7646 (tt0)
REVERT: D  207 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7182 (tpt170)
REVERT: D  237 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6286 (tp40)
REVERT: D  244 MET cc_start: 0.8647 (mtt) cc_final: 0.8371 (mtp)
REVERT: D  298 ASP cc_start: 0.7432 (m-30) cc_final: 0.7213 (m-30)
REVERT: D  300 GLN cc_start: 0.6897 (tm-30) cc_final: 0.6368 (tm-30)
REVERT: D  333 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7576 (mp)
REVERT: D  346 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7689 (mt-10)
REVERT: D  371 LEU cc_start: 0.8421 (mt) cc_final: 0.7971 (tt)
REVERT: D  413 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8324 (m)
REVERT: D  415 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8704 (ptm160)
REVERT: D  479 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8346 (p0)
REVERT: D  481 ARG cc_start: 0.7816 (ttt180) cc_final: 0.6886 (ttt90)
REVERT: D  746 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7235 (mtmm)
REVERT: D  769 MET cc_start: 0.6923 (mmm) cc_final: 0.6667 (tmm)
REVERT: D  792 MET cc_start: 0.7844 (mmm) cc_final: 0.7189 (tmm)
REVERT: D  799 GLN cc_start: 0.7505 (mp10) cc_final: 0.7150 (mp10)
REVERT: D  814 TYR cc_start: 0.7318 (p90) cc_final: 0.7039 (p90)
REVERT: D  831 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6707 (tm-30)
REVERT: F    6 THR cc_start: 0.8880 (m) cc_final: 0.8524 (t)
REVERT: F  149 PHE cc_start: 0.8415 (t80) cc_final: 0.8058 (t80)
REVERT: G   14 LYS cc_start: 0.8410 (mmpt) cc_final: 0.7406 (mtmt)
REVERT: G  105 GLN cc_start: 0.7624 (mm110) cc_final: 0.7289 (mp10)
REVERT: C   16 LYS cc_start: 0.8827 (tptt) cc_final: 0.8043 (ttpp)
REVERT: C   23 THR cc_start: 0.8496 (m) cc_final: 0.8084 (p)
REVERT: C   57 MET cc_start: 0.8264 (mtm) cc_final: 0.7983 (mtp)
REVERT: C   61 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7892 (mtmt)
REVERT: C   79 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.7066 (ptp90)
REVERT: C  160 ARG cc_start: 0.7798 (mmm160) cc_final: 0.7152 (mmt-90)
  outliers start: 66
  outliers final: 49
  residues processed: 258
  average time/residue: 0.2208
  time to fit residues: 84.5385
Evaluate side-chains
  242 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 186
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
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   58 LEU
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 H residue  275 THR
Chi-restraints excluded: chain D residue   11 ASP
Chi-restraints excluded: chain D residue   69 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  226 ASP
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
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  333 ILE
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  379 ASN
Chi-restraints excluded: chain D residue  409 HIS
Chi-restraints excluded: chain D residue  413 SER
Chi-restraints excluded: chain D residue  415 ARG
Chi-restraints excluded: chain D residue  479 ASN
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  496 SER
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  551 LEU
Chi-restraints excluded: chain D residue  564 ASP
Chi-restraints excluded: chain D residue  581 ASP
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  734 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain D residue  771 THR
Chi-restraints excluded: chain D residue  831 GLU
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain F residue   97 ASN
Chi-restraints excluded: chain F residue  124 THR
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  122 LEU
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 125 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0670
   chunk 2 optimal weight:    5.9990
   chunk 112 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 128 optimal weight:    0.7980
   chunk 104 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 76 optimal weight:    4.9990
   chunk 135 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.9322

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

Flipped N/Q/H residues before XYZ refinement:
** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 130 GLN
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.6847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12238  Z= 0.236
  Angle     :  0.620   8.434  16706  Z= 0.321
  Chirality :  0.045   0.278   1912
  Planarity :  0.005   0.107   2200
  Dihedral  :  5.078  56.530   1719
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 15.79 %
    Favored  : 79.16 %
  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: -2.41 (0.19), residues: 1572
  helix: -4.44 (0.57), residues: 31
  sheet: -0.41 (0.22), residues: 569
  loop : -2.38 (0.17), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 802 
 HIS   0.005   0.001   HIS D 200 
 PHE   0.019   0.002   PHE D 146 
 TYR   0.022   0.002   TYR H 195 
 ARG   0.004   0.000   ARG C 116 

*********************** 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
  256 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 63
    poor density    : 193
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   58 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6028 (pp)
REVERT: H   64 TYR cc_start: 0.7039 (m-80) cc_final: 0.6318 (m-80)
REVERT: H   84 PHE cc_start: 0.4700 (t80) cc_final: 0.4329 (t80)
REVERT: D   12 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.5860 (t0)
REVERT: D  206 GLU cc_start: 0.7959 (tt0) cc_final: 0.7667 (tt0)
REVERT: D  207 ARG cc_start: 0.7859 (ttt90) cc_final: 0.7458 (tpt-90)
REVERT: D  237 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.6274 (tp40)
REVERT: D  244 MET cc_start: 0.8706 (mtt) cc_final: 0.8377 (mtp)
REVERT: D  298 ASP cc_start: 0.7513 (m-30) cc_final: 0.7281 (m-30)
REVERT: D  300 GLN cc_start: 0.6907 (tm-30) cc_final: 0.6532 (tm-30)
REVERT: D  333 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7560 (mp)
REVERT: D  346 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7738 (mm-30)
REVERT: D  371 LEU cc_start: 0.8500 (mt) cc_final: 0.8048 (tt)
REVERT: D  415 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8569 (ttp80)
REVERT: D  479 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8236 (p0)
REVERT: D  481 ARG cc_start: 0.7720 (ttt180) cc_final: 0.6608 (ttt90)
REVERT: D  494 ARG cc_start: 0.6485 (tpp-160) cc_final: 0.6237 (tpp80)
REVERT: D  725 ASP cc_start: 0.7990 (t0) cc_final: 0.7648 (t0)
REVERT: D  746 LYS cc_start: 0.7552 (mmmt) cc_final: 0.7183 (mtmm)
REVERT: D  769 MET cc_start: 0.6896 (mmm) cc_final: 0.6354 (tmm)
REVERT: D  799 GLN cc_start: 0.7493 (mp10) cc_final: 0.7138 (mp10)
REVERT: G   14 LYS cc_start: 0.8424 (mmpt) cc_final: 0.7430 (mtmt)
REVERT: G  105 GLN cc_start: 0.7634 (mm110) cc_final: 0.7328 (mp10)
REVERT: C   16 LYS cc_start: 0.8883 (tptt) cc_final: 0.8072 (ttpp)
REVERT: C   23 THR cc_start: 0.8503 (m) cc_final: 0.8117 (p)
REVERT: C   57 MET cc_start: 0.8257 (mtm) cc_final: 0.8016 (mtp)
REVERT: C   79 ARG cc_start: 0.7530 (ptp-170) cc_final: 0.7096 (ptp90)
REVERT: C  160 ARG cc_start: 0.7736 (mmm160) cc_final: 0.7149 (mmt180)
  outliers start: 63
  outliers final: 50
  residues processed: 236
  average time/residue: 0.2254
  time to fit residues: 77.6194
Evaluate side-chains
  237 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 181
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 THR
Chi-restraints excluded: chain H residue   58 LEU
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  131 LEU
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  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  226 ASP
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  248 SER
Chi-restraints excluded: chain D residue  275 ILE
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  334 THR
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  415 ARG
Chi-restraints excluded: chain D residue  479 ASN
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  496 SER
Chi-restraints excluded: chain D residue  499 TYR
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  581 ASP
Chi-restraints excluded: chain D residue  589 LEU
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  601 ASN
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain D residue  771 THR
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    5 ILE
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  122 LEU
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 50 optimal weight:    6.9990
   chunk 135 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 37 optimal weight:    7.9990
   chunk 150 optimal weight:    7.9990
   chunk 125 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 12 optimal weight:   20.0000
   chunk 49 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 191 GLN
** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  94 GLN
G  78 GLN
** C  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.7575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12238  Z= 0.409
  Angle     :  0.742  10.362  16706  Z= 0.391
  Chirality :  0.048   0.225   1912
  Planarity :  0.006   0.105   2200
  Dihedral  :  5.917  56.074   1719
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 15.71 %
    Favored  : 78.15 %
  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: -2.68 (0.19), residues: 1572
  helix: -4.67 (0.46), residues: 30
  sheet: -0.60 (0.21), residues: 589
  loop : -2.61 (0.16), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 802 
 HIS   0.005   0.002   HIS D 559 
 PHE   0.028   0.003   PHE D 766 
 TYR   0.027   0.002   TYR D 436 
 ARG   0.005   0.001   ARG D 176 

*********************** 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
  280 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 203
  time to evaluate  : 1.291 
Fit side-chains
REVERT: H   53 THR cc_start: 0.5171 (m) cc_final: 0.4788 (t)
REVERT: H   64 TYR cc_start: 0.7046 (m-80) cc_final: 0.6520 (m-80)
REVERT: H  101 LYS cc_start: 0.6807 (pttt) cc_final: 0.5683 (tptt)
REVERT: D  207 ARG cc_start: 0.7961 (ttt90) cc_final: 0.7555 (tpt-90)
REVERT: D  237 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.6435 (tp40)
REVERT: D  244 MET cc_start: 0.8709 (mtt) cc_final: 0.8373 (mtp)
REVERT: D  300 GLN cc_start: 0.6874 (tm-30) cc_final: 0.6406 (tm-30)
REVERT: D  333 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7762 (mp)
REVERT: D  334 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8558 (t)
REVERT: D  346 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7900 (mm-30)
REVERT: D  371 LEU cc_start: 0.8531 (mt) cc_final: 0.7998 (tt)
REVERT: D  415 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8283 (ttp80)
REVERT: D  479 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8216 (p0)
REVERT: D  494 ARG cc_start: 0.7021 (tpp-160) cc_final: 0.6736 (tpp80)
REVERT: D  725 ASP cc_start: 0.7962 (t0) cc_final: 0.7651 (t0)
REVERT: D  746 LYS cc_start: 0.7547 (mmmt) cc_final: 0.7167 (mtmm)
REVERT: D  769 MET cc_start: 0.6995 (mmm) cc_final: 0.6500 (tmm)
REVERT: F   10 TYR cc_start: 0.8082 (t80) cc_final: 0.7340 (t80)
REVERT: F   79 LEU cc_start: 0.8570 (tt) cc_final: 0.8307 (tt)
REVERT: F  132 MET cc_start: 0.6022 (tpp) cc_final: 0.5741 (tpp)
REVERT: F  149 PHE cc_start: 0.8612 (t80) cc_final: 0.8339 (t80)
REVERT: G   14 LYS cc_start: 0.8386 (mmpt) cc_final: 0.7388 (mtmt)
REVERT: G  105 GLN cc_start: 0.7740 (mm110) cc_final: 0.7433 (mm110)
REVERT: G  144 SER cc_start: 0.8575 (p) cc_final: 0.8325 (t)
REVERT: C   16 LYS cc_start: 0.8940 (tptt) cc_final: 0.8113 (ttpp)
REVERT: C   23 THR cc_start: 0.8548 (m) cc_final: 0.8156 (p)
REVERT: C   79 ARG cc_start: 0.7619 (ptp-170) cc_final: 0.7253 (ptp-110)
REVERT: C   80 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7888 (mm-30)
REVERT: C  200 MET cc_start: 0.7472 (ppp) cc_final: 0.7267 (tmm)
  outliers start: 77
  outliers final: 57
  residues processed: 257
  average time/residue: 0.2190
  time to fit residues: 83.3903
Evaluate side-chains
  247 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 185
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
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   58 LEU
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   71 PHE
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  130 ILE
Chi-restraints excluded: chain H residue  167 ASP
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  212 THR
Chi-restraints excluded: chain H residue  214 SER
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain H residue  275 THR
Chi-restraints excluded: chain D residue   69 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  226 ASP
Chi-restraints excluded: chain D residue  234 ARG
Chi-restraints excluded: chain D residue  237 GLN
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  333 ILE
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  409 HIS
Chi-restraints excluded: chain D residue  415 ARG
Chi-restraints excluded: chain D residue  479 ASN
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  499 TYR
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  564 ASP
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  601 ASN
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  734 VAL
Chi-restraints excluded: chain D residue  770 VAL
Chi-restraints excluded: chain D residue  771 THR
Chi-restraints excluded: chain D residue  811 VAL
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    5 ILE
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  122 LEU
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  153 THR
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 145 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 110 optimal weight:   10.0000
   chunk 127 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 150 optimal weight:    0.1980
   chunk 94 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 191 GLN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  36 GLN
G  22 ASN
G  97 ASN
C  17 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.7464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12238  Z= 0.158
  Angle     :  0.605  11.918  16706  Z= 0.306
  Chirality :  0.044   0.258   1912
  Planarity :  0.005   0.117   2200
  Dihedral  :  4.924  56.840   1719
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 18.66 %
    Favored  : 77.84 %
  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: -2.31 (0.19), residues: 1572
  helix: -4.37 (0.58), residues: 30
  sheet: -0.40 (0.21), residues: 595
  loop : -2.32 (0.17), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 508 
 HIS   0.003   0.001   HIS D 200 
 PHE   0.026   0.002   PHE D 766 
 TYR   0.021   0.001   TYR D 436 
 ARG   0.008   0.000   ARG C 160 

*********************** 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
  236 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 193
  time to evaluate  : 1.195 
Fit side-chains
REVERT: H   64 TYR cc_start: 0.6762 (m-80) cc_final: 0.6057 (m-80)
REVERT: H  101 LYS cc_start: 0.6870 (pttt) cc_final: 0.5722 (tptt)
REVERT: D  103 HIS cc_start: 0.7233 (t70) cc_final: 0.6008 (t-90)
REVERT: D  181 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8122 (p)
REVERT: D  206 GLU cc_start: 0.7921 (tt0) cc_final: 0.7604 (tt0)
REVERT: D  237 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.6319 (tp40)
REVERT: D  244 MET cc_start: 0.8638 (mtt) cc_final: 0.8298 (mtp)
REVERT: D  298 ASP cc_start: 0.8113 (m-30) cc_final: 0.7911 (t0)
REVERT: D  333 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7435 (mp)
REVERT: D  346 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7960 (mm-30)
REVERT: D  371 LEU cc_start: 0.8532 (mt) cc_final: 0.8057 (tt)
REVERT: D  415 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8496 (ttp80)
REVERT: D  479 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8073 (p0)
REVERT: D  481 ARG cc_start: 0.7555 (ttt180) cc_final: 0.6453 (ttt90)
REVERT: D  494 ARG cc_start: 0.6823 (tpp-160) cc_final: 0.6571 (tpp80)
REVERT: D  725 ASP cc_start: 0.7955 (t0) cc_final: 0.7644 (t0)
REVERT: D  746 LYS cc_start: 0.7488 (mmmt) cc_final: 0.7147 (mtmm)
REVERT: D  769 MET cc_start: 0.6882 (mmm) cc_final: 0.6360 (tmm)
REVERT: F   10 TYR cc_start: 0.7956 (t80) cc_final: 0.7141 (t80)
REVERT: F   17 SER cc_start: 0.8366 (t) cc_final: 0.7732 (p)
REVERT: F  132 MET cc_start: 0.6099 (tpp) cc_final: 0.5776 (tpp)
REVERT: F  149 PHE cc_start: 0.8417 (t80) cc_final: 0.8176 (t80)
REVERT: G   14 LYS cc_start: 0.8392 (mmpt) cc_final: 0.7411 (mtmt)
REVERT: G  144 SER cc_start: 0.8463 (p) cc_final: 0.8175 (t)
REVERT: C   16 LYS cc_start: 0.8828 (tptt) cc_final: 0.7986 (ttpp)
REVERT: C   23 THR cc_start: 0.8547 (m) cc_final: 0.8176 (p)
REVERT: C  160 ARG cc_start: 0.7136 (mmm160) cc_final: 0.5919 (mmp80)
  outliers start: 43
  outliers final: 33
  residues processed: 224
  average time/residue: 0.2063
  time to fit residues: 69.4381
Evaluate side-chains
  217 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 179
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 ASN
Chi-restraints excluded: chain H residue   58 LEU
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  212 THR
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  181 THR
Chi-restraints excluded: chain D residue  226 ASP
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  248 SER
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  415 ARG
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  479 ASN
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  499 TYR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  564 ASP
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  634 ASN
Chi-restraints excluded: chain D residue  686 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  124 THR
Chi-restraints excluded: chain F residue  142 HIS
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  122 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 118 optimal weight:    4.9990
   chunk 136 optimal weight:    6.9990
   chunk 144 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 191 GLN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.7793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12238  Z= 0.319
  Angle     :  0.689  11.431  16706  Z= 0.357
  Chirality :  0.046   0.247   1912
  Planarity :  0.006   0.116   2200
  Dihedral  :  5.391  57.610   1719
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 19.44 %
    Favored  : 76.52 %
  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: -2.45 (0.19), residues: 1572
  helix: -5.07 (0.29), residues: 24
  sheet: -0.43 (0.22), residues: 586
  loop : -2.45 (0.17), residues: 962

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 541 
 HIS   0.005   0.001   HIS D 200 
 PHE   0.033   0.002   PHE D 766 
 TYR   0.023   0.002   TYR D 436 
 ARG   0.006   0.001   ARG C 160 

*********************** 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
  237 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 187
  time to evaluate  : 1.410 
Fit side-chains
REVERT: H   53 THR cc_start: 0.5236 (m) cc_final: 0.4852 (t)
REVERT: H   64 TYR cc_start: 0.6912 (m-80) cc_final: 0.6131 (m-80)
REVERT: H   84 PHE cc_start: 0.4332 (t80) cc_final: 0.3791 (t80)
REVERT: H  101 LYS cc_start: 0.6867 (pttt) cc_final: 0.5756 (tptt)
REVERT: D  103 HIS cc_start: 0.7347 (t70) cc_final: 0.6273 (t-90)
REVERT: D  181 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8277 (p)
REVERT: D  206 GLU cc_start: 0.7955 (tt0) cc_final: 0.7618 (tt0)
REVERT: D  237 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.6262 (tp40)
REVERT: D  244 MET cc_start: 0.8644 (mtt) cc_final: 0.8278 (mtp)
REVERT: D  298 ASP cc_start: 0.8149 (m-30) cc_final: 0.7928 (t0)
REVERT: D  333 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7572 (mp)
REVERT: D  346 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7849 (mm-30)
REVERT: D  371 LEU cc_start: 0.8532 (mt) cc_final: 0.8000 (tt)
REVERT: D  415 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8434 (ttp80)
REVERT: D  479 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8025 (p0)
REVERT: D  494 ARG cc_start: 0.6936 (tpp-160) cc_final: 0.6641 (tpp80)
REVERT: D  725 ASP cc_start: 0.7930 (t0) cc_final: 0.7665 (t0)
REVERT: D  746 LYS cc_start: 0.7525 (mmmt) cc_final: 0.7215 (mtmm)
REVERT: D  769 MET cc_start: 0.7036 (mmm) cc_final: 0.6629 (tmm)
REVERT: F   10 TYR cc_start: 0.7921 (t80) cc_final: 0.7298 (t80)
REVERT: F   17 SER cc_start: 0.8416 (t) cc_final: 0.7724 (p)
REVERT: F  132 MET cc_start: 0.6247 (tpp) cc_final: 0.5943 (tpp)
REVERT: F  149 PHE cc_start: 0.8580 (t80) cc_final: 0.8272 (t80)
REVERT: G   14 LYS cc_start: 0.8401 (mmpt) cc_final: 0.7408 (mtmt)
REVERT: G  144 SER cc_start: 0.8490 (p) cc_final: 0.8272 (t)
REVERT: C   16 LYS cc_start: 0.8875 (tptt) cc_final: 0.8086 (ttpt)
REVERT: C   23 THR cc_start: 0.8525 (m) cc_final: 0.8152 (p)
REVERT: C   80 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7916 (mm-30)
REVERT: C  130 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8094 (mmtm)
REVERT: C  160 ARG cc_start: 0.7144 (mmm160) cc_final: 0.5979 (mmp80)
REVERT: C  200 MET cc_start: 0.8442 (tmm) cc_final: 0.8116 (ppp)
  outliers start: 50
  outliers final: 40
  residues processed: 225
  average time/residue: 0.2144
  time to fit residues: 73.1230
Evaluate side-chains
  227 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 182
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 ASN
Chi-restraints excluded: chain H residue   58 LEU
Chi-restraints excluded: chain H residue  109 LEU
Chi-restraints excluded: chain H residue  135 ASN
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  212 THR
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  181 THR
Chi-restraints excluded: chain D residue  226 ASP
Chi-restraints excluded: chain D residue  237 GLN
Chi-restraints excluded: chain D residue  248 SER
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  333 ILE
Chi-restraints excluded: chain D residue  415 ARG
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  479 ASN
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  499 TYR
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  564 ASP
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  634 ASN
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  771 THR
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain F residue   18 VAL
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  122 LEU
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   67 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    3.9990
   chunk 140 optimal weight:    7.9990
   chunk 144 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 110 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 126 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9990
   chunk 139 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 262 GLN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 815 GLN
G  97 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.8206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  12238  Z= 0.372
  Angle     :  0.722  11.927  16706  Z= 0.379
  Chirality :  0.047   0.240   1912
  Planarity :  0.006   0.117   2200
  Dihedral  :  5.883  55.930   1719
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 19.21 %
    Favored  : 76.13 %
  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: -2.58 (0.19), residues: 1572
  helix: -4.02 (0.70), residues: 18
  sheet: -0.50 (0.21), residues: 590
  loop : -2.61 (0.17), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 198 
 HIS   0.006   0.002   HIS D 200 
 PHE   0.031   0.002   PHE D 766 
 TYR   0.026   0.002   TYR D 436 
 ARG   0.006   0.001   ARG C 160 

*********************** 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
  241 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 183
  time to evaluate  : 1.307 
Fit side-chains
REVERT: H   53 THR cc_start: 0.5700 (m) cc_final: 0.5337 (t)
REVERT: H   59 GLN cc_start: 0.5576 (OUTLIER) cc_final: 0.4919 (pm20)
REVERT: H   64 TYR cc_start: 0.6791 (m-80) cc_final: 0.6091 (m-80)
REVERT: H  101 LYS cc_start: 0.6925 (pttt) cc_final: 0.5857 (tptt)
REVERT: H  156 VAL cc_start: 0.8267 (t) cc_final: 0.7928 (m)
REVERT: D  103 HIS cc_start: 0.7434 (t70) cc_final: 0.6359 (t-90)
REVERT: D  163 TYR cc_start: 0.6528 (m-80) cc_final: 0.6106 (m-80)
REVERT: D  181 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8214 (p)
REVERT: D  237 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.6392 (tp40)
REVERT: D  244 MET cc_start: 0.8646 (mtt) cc_final: 0.8299 (mtp)
REVERT: D  333 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7690 (mp)
REVERT: D  334 THR cc_start: 0.8774 (p) cc_final: 0.8546 (t)
REVERT: D  346 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7868 (mm-30)
REVERT: D  371 LEU cc_start: 0.8602 (mt) cc_final: 0.8087 (tt)
REVERT: D  415 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8379 (ttp80)
REVERT: D  479 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8111 (p0)
REVERT: D  494 ARG cc_start: 0.7268 (tpp-160) cc_final: 0.6917 (tpp80)
REVERT: D  725 ASP cc_start: 0.7858 (t0) cc_final: 0.7603 (t0)
REVERT: D  746 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7143 (mtmm)
REVERT: D  769 MET cc_start: 0.7006 (mmm) cc_final: 0.6713 (tmm)
REVERT: F   10 TYR cc_start: 0.7973 (t80) cc_final: 0.7461 (t80)
REVERT: F  132 MET cc_start: 0.6258 (tpp) cc_final: 0.5980 (tpp)
REVERT: F  149 PHE cc_start: 0.8614 (t80) cc_final: 0.8313 (t80)
REVERT: G   14 LYS cc_start: 0.8375 (mmpt) cc_final: 0.7396 (mtmt)
REVERT: G  144 SER cc_start: 0.8647 (p) cc_final: 0.8405 (t)
REVERT: C   16 LYS cc_start: 0.8900 (tptt) cc_final: 0.8053 (ttpp)
REVERT: C   23 THR cc_start: 0.8528 (m) cc_final: 0.8173 (p)
REVERT: C   62 GLU cc_start: 0.8279 (pp20) cc_final: 0.8075 (pp20)
REVERT: C   80 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7793 (mm-30)
REVERT: C  160 ARG cc_start: 0.7241 (mmm160) cc_final: 0.5891 (mmp80)
REVERT: C  200 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7850 (ppp)
  outliers start: 58
  outliers final: 48
  residues processed: 228
  average time/residue: 0.2007
  time to fit residues: 69.0584
Evaluate side-chains
  233 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 178
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 ASN
Chi-restraints excluded: chain H residue   58 LEU
Chi-restraints excluded: chain H residue   59 GLN
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  135 ASN
Chi-restraints excluded: chain H residue  167 ASP
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  212 THR
Chi-restraints excluded: chain H residue  214 SER
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  181 THR
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  214 SER
Chi-restraints excluded: chain D residue  226 ASP
Chi-restraints excluded: chain D residue  237 GLN
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  333 ILE
Chi-restraints excluded: chain D residue  369 THR
Chi-restraints excluded: chain D residue  413 SER
Chi-restraints excluded: chain D residue  415 ARG
Chi-restraints excluded: chain D residue  479 ASN
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  499 TYR
Chi-restraints excluded: chain D residue  523 THR
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  564 ASP
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  601 ASN
Chi-restraints excluded: chain D residue  634 ASN
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  771 THR
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain F residue   18 VAL
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  122 LEU
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   67 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
Chi-restraints excluded: chain C residue  200 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 148 optimal weight:    0.0370
   chunk 90 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 102 optimal weight:    1.9990
   chunk 155 optimal weight:    2.9990
   chunk 143 optimal weight:    0.7980
   chunk 123 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   chunk 95 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.1262

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 191 GLN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  22 ASN
G  97 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.8093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12238  Z= 0.177
  Angle     :  0.621  12.514  16706  Z= 0.315
  Chirality :  0.044   0.238   1912
  Planarity :  0.006   0.127   2200
  Dihedral  :  5.150  61.975   1719
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.92 %
    Favored  : 75.66 %
  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 (0.20), residues: 1572
  helix: -3.76 (0.84), residues: 18
  sheet: -0.37 (0.21), residues: 594
  loop : -2.31 (0.17), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 198 
 HIS   0.003   0.001   HIS D 257 
 PHE   0.028   0.002   PHE D 766 
 TYR   0.022   0.001   TYR D 436 
 ARG   0.006   0.000   ARG C 160 

********************** 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
  222 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 180
  time to evaluate  : 1.342 
Fit side-chains
REVERT: H   59 GLN cc_start: 0.5529 (OUTLIER) cc_final: 0.4765 (pm20)
REVERT: H  101 LYS cc_start: 0.6966 (pttt) cc_final: 0.5887 (tptt)
REVERT: H  156 VAL cc_start: 0.8153 (t) cc_final: 0.7778 (m)
REVERT: D  181 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8094 (p)
REVERT: D  206 GLU cc_start: 0.7979 (tt0) cc_final: 0.7774 (tt0)
REVERT: D  237 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.6216 (tp40)
REVERT: D  244 MET cc_start: 0.8605 (mtt) cc_final: 0.8268 (mtp)
REVERT: D  333 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7411 (mp)
REVERT: D  346 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7892 (mm-30)
REVERT: D  371 LEU cc_start: 0.8554 (mt) cc_final: 0.8024 (tt)
REVERT: D  415 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8249 (ttp80)
REVERT: D  479 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7988 (p0)
REVERT: D  494 ARG cc_start: 0.6992 (tpp-160) cc_final: 0.6694 (tpp80)
REVERT: D  725 ASP cc_start: 0.7923 (t0) cc_final: 0.7709 (t0)
REVERT: D  746 LYS cc_start: 0.7479 (mmmt) cc_final: 0.7145 (mtmm)
REVERT: D  769 MET cc_start: 0.7011 (mmm) cc_final: 0.6575 (tmm)
REVERT: F   10 TYR cc_start: 0.7883 (t80) cc_final: 0.7318 (t80)
REVERT: F  132 MET cc_start: 0.6229 (tpp) cc_final: 0.5944 (tpp)
REVERT: F  149 PHE cc_start: 0.8504 (t80) cc_final: 0.8217 (t80)
REVERT: G   14 LYS cc_start: 0.8377 (mmpt) cc_final: 0.7433 (mtmt)
REVERT: G  129 THR cc_start: 0.8767 (p) cc_final: 0.8487 (t)
REVERT: G  144 SER cc_start: 0.8566 (p) cc_final: 0.8281 (t)
REVERT: C   16 LYS cc_start: 0.8802 (tptt) cc_final: 0.8003 (ttpp)
REVERT: C   23 THR cc_start: 0.8525 (m) cc_final: 0.8170 (p)
REVERT: C   62 GLU cc_start: 0.8226 (pp20) cc_final: 0.7990 (pp20)
REVERT: C   80 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7621 (mm-30)
REVERT: C  129 GLU cc_start: 0.8339 (tp30) cc_final: 0.8134 (tp30)
REVERT: C  160 ARG cc_start: 0.7285 (mmm160) cc_final: 0.5949 (mmp80)
  outliers start: 42
  outliers final: 32
  residues processed: 211
  average time/residue: 0.2054
  time to fit residues: 65.2941
Evaluate side-chains
  212 residues out of total 1299 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 174
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 ASN
Chi-restraints excluded: chain H residue   58 LEU
Chi-restraints excluded: chain H residue   59 GLN
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  109 LEU
Chi-restraints excluded: chain H residue  135 ASN
Chi-restraints excluded: chain H residue  183 LEU
Chi-restraints excluded: chain H residue  187 CYS
Chi-restraints excluded: chain H residue  212 THR
Chi-restraints excluded: chain H residue  250 LEU
Chi-restraints excluded: chain D residue   69 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  181 THR
Chi-restraints excluded: chain D residue  226 ASP
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  415 ARG
Chi-restraints excluded: chain D residue  479 ASN
Chi-restraints excluded: chain D residue  489 THR
Chi-restraints excluded: chain D residue  499 TYR
Chi-restraints excluded: chain D residue  518 GLN
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  564 ASP
Chi-restraints excluded: chain D residue  592 VAL
Chi-restraints excluded: chain D residue  634 ASN
Chi-restraints excluded: chain D residue  686 VAL
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue  124 THR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 114 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 123 optimal weight:    0.0270
   chunk 51 optimal weight:    3.9990
   chunk 127 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    2.8046

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

Flipped N/Q/H residues before XYZ refinement:
** H  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 191 GLN
** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 661 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.169741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.159700 restraints weight = 25277.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.148824 restraints weight = 39400.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.142623 restraints weight = 32678.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3453
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3450
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.8253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12238  Z= 0.318
  Angle     :  0.696  11.852  16706  Z= 0.357
  Chirality :  0.046   0.235   1912
  Planarity :  0.006   0.135   2200
  Dihedral  :  5.470  65.149   1719
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 20.53 %
    Favored  : 75.51 %
  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: -2.37 (0.20), residues: 1572
  helix: -4.71 (0.58), residues: 12
  sheet: -0.44 (0.22), residues: 596
  loop : -2.42 (0.17), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 198 
 HIS   0.005   0.001   HIS D 200 
 PHE   0.030   0.002   PHE D 766 
 TYR   0.023   0.002   TYR D 436 
 ARG   0.006   0.001   ARG C 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2489.95 seconds
wall clock time: 46 minutes 7.96 seconds (2767.96 seconds total)