Starting phenix.real_space_refine
on Wed Mar  4 23:06:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b70_12063/03_2026/7b70_12063_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b70_12063/03_2026/7b70_12063.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b70_12063/03_2026/7b70_12063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b70_12063/03_2026/7b70_12063.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b70_12063/03_2026/7b70_12063_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b70_12063/03_2026/7b70_12063_neut.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      95      5.16       5
     C   10934      2.51       5
     N    2914      2.21       5
     O    3141      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17084
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1337
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 7, 'TRANS': 157}
    Chain: "B"
      Number of atoms: 1226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1226
          Classifications: {'peptide': 151}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 147}
    Chain: "C"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1204
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
    Chain: "D"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1741
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207}
    Chain: "E"
      Number of atoms: 1177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1177
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
    Chain: "F"
      Number of atoms: 1333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1333
          Classifications: {'peptide': 164}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 159}
    Chain: "G"
      Number of atoms: 1363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1363
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 7, 'TRANS': 161}
    Chain: "H"
      Number of atoms: 1089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1089
          Classifications: {'peptide': 138}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 133}
    Chain: "I"
      Number of atoms: 1710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1710
          Classifications: {'peptide': 208}
          Link IDs: {'PTRANS': 3, 'TRANS': 204}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 4904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4904
          Classifications: {'peptide': 614}
          Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 592}
          Chain breaks: 4
  Time building chain proxies: 3.57, per 1000 atoms: 0.21
  Number of scatterers: 17084
  At special positions: 0
  Unit cell: (204.793, 283.946, 113.076, 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      95     16.00
     O    3141      8.00
     N    2914      7.00
     C   10934      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.70
  Conformation dependent library (CDL) restraints added in 765.3 milliseconds
  

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4058

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 12 sheets defined
      53.2% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 15
      No H-bonds generated for 'chain 'A' and resid 13 through 15'
    Processing helix  chain 'A' and resid 16 through 33
      removed outlier: 3.783A  pdb=" N   LEU A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 62
      removed outlier: 4.250A  pdb=" N   GLU A  56 " --> pdb=" O   MET A  52 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ASP A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 85
    Processing helix  chain 'A' and resid 126 through 140
    Processing helix  chain 'A' and resid 151 through 155
    Processing helix  chain 'B' and resid 3 through 17
      removed outlier: 4.318A  pdb=" N   PHE B   7 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 42
    Processing helix  chain 'B' and resid 58 through 70
    Processing helix  chain 'B' and resid 93 through 98
      removed outlier: 3.699A  pdb=" N   ARG B  98 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 115
      removed outlier: 4.126A  pdb=" N   PHE B 115 " --> pdb=" O   LYS B 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 53
    Processing helix  chain 'C' and resid 93 through 103
    Processing helix  chain 'C' and resid 103 through 109
    Processing helix  chain 'C' and resid 123 through 135
    Processing helix  chain 'D' and resid 81 through 88
    Processing helix  chain 'D' and resid 104 through 121
      Proline residue:  D 117  - end of helix
    Processing helix  chain 'D' and resid 166 through 182
    Processing helix  chain 'D' and resid 195 through 211
    Processing helix  chain 'E' and resid 26 through 55
      removed outlier: 3.606A  pdb=" N   HIS E  42 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ALA E  43 " --> pdb=" O   PHE E  39 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   GLU E  50 " --> pdb=" O   ASP E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 110
      removed outlier: 3.890A  pdb=" N   ASN E  96 " --> pdb=" O   GLU E  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 137
    Processing helix  chain 'F' and resid 32 through 50
    Processing helix  chain 'F' and resid 52 through 78
      removed outlier: 4.041A  pdb=" N   ARG F  70 " --> pdb=" O   ASP F  66 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   ASP F  73 " --> pdb=" O   THR F  69 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   VAL F  77 " --> pdb=" O   ASP F  73 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ARG F  78 " --> pdb=" O   LEU F  74 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 104
    Processing helix  chain 'F' and resid 129 through 133
      removed outlier: 3.623A  pdb=" N   THR F 132 " --> pdb=" O   LEU F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 145 through 161
    Processing helix  chain 'F' and resid 181 through 191
    Processing helix  chain 'G' and resid 13 through 32
      removed outlier: 3.554A  pdb=" N   LEU G  17 " --> pdb=" O   ASN G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 34 through 61
      removed outlier: 3.552A  pdb=" N   MET G  51 " --> pdb=" O   TYR G  47 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ARG G  52 " --> pdb=" O   ASN G  48 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   GLU G  55 " --> pdb=" O   MET G  51 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 68 through 84
      removed outlier: 3.605A  pdb=" N   THR G  72 " --> pdb=" O   GLU G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 116 through 120
      removed outlier: 3.705A  pdb=" N   THR G 120 " --> pdb=" O   PRO G 117 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 123 through 125
      No H-bonds generated for 'chain 'G' and resid 123 through 125'
    Processing helix  chain 'G' and resid 126 through 139
    Processing helix  chain 'G' and resid 150 through 154
      removed outlier: 3.712A  pdb=" N   GLY G 154 " --> pdb=" O   GLN G 151 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 41
    Processing helix  chain 'H' and resid 91 through 111
      removed outlier: 3.884A  pdb=" N   VAL H  95 " --> pdb=" O   ARG H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 123 through 138
    Processing helix  chain 'I' and resid 356 through 385
      Proline residue:  I 371  - end of helix
    Processing helix  chain 'I' and resid 425 through 436
    Processing helix  chain 'I' and resid 440 through 453
    Processing helix  chain 'I' and resid 460 through 479
      removed outlier: 4.142A  pdb=" N   TYR I 464 " --> pdb=" O   ALA I 460 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 482 through 492
    Processing helix  chain 'I' and resid 493 through 500
      removed outlier: 3.519A  pdb=" N   THR I 498 " --> pdb=" O   VAL I 494 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL I 499 " --> pdb=" O   CYS I 495 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 502 through 520
    Processing helix  chain 'I' and resid 522 through 535
      removed outlier: 3.701A  pdb=" N   VAL I 526 " --> pdb=" O   LEU I 522 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 539 through 557
      removed outlier: 3.557A  pdb=" N   THR I 556 " --> pdb=" O   CYS I 552 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLN I 557 " --> pdb=" O   PHE I 553 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 562 through 578
      removed outlier: 3.519A  pdb=" N   LEU I 570 " --> pdb=" O   PHE I 566 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 580 through 598
    Processing helix  chain 'J' and resid 26 through 33
    Processing helix  chain 'J' and resid 33 through 46
      removed outlier: 4.264A  pdb=" N   SER J  43 " --> pdb=" O   ALA J  39 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LEU J  44 " --> pdb=" O   PHE J  40 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 85 through 94
      removed outlier: 3.565A  pdb=" N   HIS J  94 " --> pdb=" O   LEU J  90 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 111 through 135
      removed outlier: 5.248A  pdb=" N   GLU J 133 " --> pdb=" O   ASN J 129 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   ARG J 134 " --> pdb=" O   THR J 130 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 154 through 169
    Processing helix  chain 'J' and resid 180 through 215
      removed outlier: 5.077A  pdb=" N   GLY J 186 " --> pdb=" O   GLU J 182 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 222 through 239
    Processing helix  chain 'J' and resid 243 through 259
    Processing helix  chain 'J' and resid 265 through 287
      removed outlier: 4.178A  pdb=" N   ILE J 269 " --> pdb=" O   ASN J 265 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 289 through 308
      removed outlier: 3.859A  pdb=" N   VAL J 308 " --> pdb=" O   HIS J 304 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 318 through 339
    Processing helix  chain 'J' and resid 341 through 347
      removed outlier: 3.841A  pdb=" N   GLN J 346 " --> pdb=" O   ALA J 342 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 349 through 374
      removed outlier: 4.324A  pdb=" N   HIS J 353 " --> pdb=" O   GLY J 349 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   LYS J 354 " --> pdb=" O   ILE J 350 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 408 through 422
    Processing helix  chain 'J' and resid 425 through 442
      removed outlier: 4.036A  pdb=" N   ILE J 429 " --> pdb=" O   SER J 425 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 445 through 463
    Processing helix  chain 'J' and resid 464 through 483
      removed outlier: 3.605A  pdb=" N   ALA J 468 " --> pdb=" O   ASP J 464 " (cutoff:3.500A)
      Proline residue:  J 477  - end of helix
    Processing helix  chain 'J' and resid 484 through 503
      removed outlier: 3.883A  pdb=" N   THR J 489 " --> pdb=" O   THR J 485 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LYS J 494 " --> pdb=" O   ASP J 490 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 504 through 518
      removed outlier: 3.725A  pdb=" N   LEU J 518 " --> pdb=" O   GLU J 514 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 523 through 539
    Processing helix  chain 'J' and resid 550 through 560
    Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92
      removed outlier: 3.731A  pdb=" N   VAL A 163 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU A 103 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU A 161 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   GLU A 160 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS A 164 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLN A 145 " --> pdb=" O   LYS A 164 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A 166 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   GLU A 143 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87
      removed outlier: 3.597A  pdb=" N   TYR B  86 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 20
      removed outlier: 6.908A  pdb=" N   ILE C   8 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   TYR C  18 " --> pdb=" O   LEU C   6 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   LEU C   6 " --> pdb=" O   TYR C  18 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASN C   5 " --> pdb=" O   ASN C  85 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TYR C  64 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR C  63 " --> pdb=" O   GLU D 138 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   GLU D 135 " --> pdb=" O   CYS D 146 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR D 143 " --> pdb=" O   SER D 159 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE D   8 " --> pdb=" O   ILE D  16 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32
      removed outlier: 4.071A  pdb=" N   LYS D  30 " --> pdb=" O   LEU D  96 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU D  96 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA D  65 " --> pdb=" O   LYS D  97 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   SER D  99 " --> pdb=" O   LEU D  63 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   LEU D  63 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   VAL D  64 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL D  71 " --> pdb=" O   VAL D  64 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 40 through 43
    Processing sheet with id=AA6, first strand: chain 'E' and resid 15 through 20
      removed outlier: 3.583A  pdb=" N   TYR E   5 " --> pdb=" O   VAL E  85 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE E  83 " --> pdb=" O   VAL E   7 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   HIS E  86 " --> pdb=" O   PHE E  70 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 110 through 113
      removed outlier: 3.509A  pdb=" N   ILE F 124 " --> pdb=" O   LYS F 110 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 99 through 100
      removed outlier: 3.505A  pdb=" N   PHE G 100 " --> pdb=" O   VAL G 162 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 99 through 100
      removed outlier: 3.505A  pdb=" N   PHE G 100 " --> pdb=" O   VAL G 162 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   GLU G 159 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   GLU G 142 " --> pdb=" O   VAL G 165 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 8
      removed outlier: 3.677A  pdb=" N   TYR H  61 " --> pdb=" O   ILE H  68 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   GLY H  70 " --> pdb=" O   LEU H  59 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU H  59 " --> pdb=" O   GLY H  70 " (cutoff:3.500A)
      removed outlier: 8.997A  pdb=" N   VAL H  72 " --> pdb=" O   LEU H  57 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   LEU H  57 " --> pdb=" O   VAL H  72 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'J' and resid 55 through 56
      removed outlier: 4.271A  pdb=" N   VAL J  99 " --> pdb=" O   LEU J  19 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL J 101 " --> pdb=" O   GLY J  21 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU J 102 " --> pdb=" O   CYS J 139 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL J 141 " --> pdb=" O   LEU J 102 " (cutoff:3.500A)
      removed outlier: 9.141A  pdb=" N   PHE J 176 " --> pdb=" O   LEU J 138 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   LEU J 140 " --> pdb=" O   PHE J 176 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   LEU J 178 " --> pdb=" O   LEU J 140 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   LEU J 142 " --> pdb=" O   LEU J 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'J' and resid 602 through 603
      removed outlier: 4.495A  pdb=" N   VAL J 602 " --> pdb=" O   TYR J 678 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   TYR J 678 " --> pdb=" O   VAL J 602 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    900 hydrogen bonds defined for protein.
    2634 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.70

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4504
        1.33 -     1.45: 3567
        1.45 -     1.58: 9213
        1.58 -     1.70: 0
        1.70 -     1.82: 152
  Bond restraints: 17436
  Sorted by residual:
  bond pdb=" N   VAL H  39 "
       pdb=" CA  VAL H  39 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.043 1.08e-02 8.57e+03 1.59e+01
  bond pdb=" C   GLU F 127 "
       pdb=" N   PRO F 128 "
    ideal  model  delta    sigma   weight residual
    1.334  1.292  0.042 1.11e-02 8.12e+03 1.41e+01
  bond pdb=" N   GLN I 557 "
       pdb=" CA  GLN I 557 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 9.60e-03 1.09e+04 1.12e+01
  bond pdb=" C   HIS D  61 "
       pdb=" N   VAL D  62 "
    ideal  model  delta    sigma   weight residual
    1.334  1.292  0.041 1.24e-02 6.50e+03 1.11e+01
  bond pdb=" C   TRP C 115 "
       pdb=" N   THR C 116 "
    ideal  model  delta    sigma   weight residual
    1.330  1.282  0.048 1.47e-02 4.63e+03 1.09e+01
  ... (remaining 17431 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 22916
        2.91 -     5.83: 590
        5.83 -     8.74: 64
        8.74 -    11.66: 7
       11.66 -    14.57: 2
  Bond angle restraints: 23579
  Sorted by residual:
  angle pdb=" N   GLU H  40 "
        pdb=" CA  GLU H  40 "
        pdb=" C   GLU H  40 "
      ideal   model   delta    sigma   weight residual
     112.54  103.73    8.81 1.22e+00 6.72e-01 5.21e+01
  angle pdb=" N   VAL H  39 "
        pdb=" CA  VAL H  39 "
        pdb=" C   VAL H  39 "
      ideal   model   delta    sigma   weight residual
     113.42  105.30    8.12 1.17e+00 7.31e-01 4.81e+01
  angle pdb=" N   VAL I 569 "
        pdb=" CA  VAL I 569 "
        pdb=" C   VAL I 569 "
      ideal   model   delta    sigma   weight residual
     111.00  104.39    6.61 1.09e+00 8.42e-01 3.68e+01
  angle pdb=" N   LEU H  44 "
        pdb=" CA  LEU H  44 "
        pdb=" C   LEU H  44 "
      ideal   model   delta    sigma   weight residual
     113.15  106.07    7.08 1.19e+00 7.06e-01 3.54e+01
  angle pdb=" N   ILE E  40 "
        pdb=" CA  ILE E  40 "
        pdb=" C   ILE E  40 "
      ideal   model   delta    sigma   weight residual
     111.44  104.39    7.05 1.34e+00 5.57e-01 2.76e+01
  ... (remaining 23574 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 9261
       17.82 -    35.64: 967
       35.64 -    53.46: 229
       53.46 -    71.28: 55
       71.28 -    89.10: 15
  Dihedral angle restraints: 10527
    sinusoidal: 4286
      harmonic: 6241
  Sorted by residual:
  dihedral pdb=" CA  ILE D 214 "
           pdb=" C   ILE D 214 "
           pdb=" N   SER D 215 "
           pdb=" CA  SER D 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.32   39.68     0      5.00e+00 4.00e-02 6.30e+01
  dihedral pdb=" CA  ILE F 134 "
           pdb=" C   ILE F 134 "
           pdb=" N   SER F 135 "
           pdb=" CA  SER F 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -141.08  -38.92     0      5.00e+00 4.00e-02 6.06e+01
  dihedral pdb=" C   VAL H  38 "
           pdb=" N   VAL H  38 "
           pdb=" CA  VAL H  38 "
           pdb=" CB  VAL H  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.89   15.89     0      2.50e+00 1.60e-01 4.04e+01
  ... (remaining 10524 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 2231
       0.083 -    0.165: 368
       0.165 -    0.248: 37
       0.248 -    0.331: 8
       0.331 -    0.414: 6
  Chirality restraints: 2650
  Sorted by residual:
  chirality pdb=" CB  ILE F 134 "
            pdb=" CA  ILE F 134 "
            pdb=" CG1 ILE F 134 "
            pdb=" CG2 ILE F 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.41 2.00e-01 2.50e+01 4.28e+00
  chirality pdb=" CG  LEU D 197 "
            pdb=" CB  LEU D 197 "
            pdb=" CD1 LEU D 197 "
            pdb=" CD2 LEU D 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.18   -0.41 2.00e-01 2.50e+01 4.16e+00
  chirality pdb=" CA  HIS I 567 "
            pdb=" N   HIS I 567 "
            pdb=" C   HIS I 567 "
            pdb=" CB  HIS I 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.14e+00
  ... (remaining 2647 not shown)

  Planarity restraints: 3009
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E  41 "   -0.028 2.00e-02 2.50e+03   5.76e-02 3.32e+01
        pdb=" C   ALA E  41 "    0.100 2.00e-02 2.50e+03
        pdb=" O   ALA E  41 "   -0.039 2.00e-02 2.50e+03
        pdb=" N   HIS E  42 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 117 "   -0.050 5.00e-02 4.00e+02   7.56e-02 9.14e+00
        pdb=" N   PRO A 118 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 118 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 118 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 136 "   -0.050 5.00e-02 4.00e+02   7.49e-02 8.98e+00
        pdb=" N   PRO F 137 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO F 137 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO F 137 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 3006 not shown)

  Histogram of nonbonded interaction distances:
        0.46 -     1.35: 10
        1.35 -     2.24: 76
        2.24 -     3.13: 15946
        3.13 -     4.01: 49639
        4.01 -     4.90: 85044
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 150715
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS H  31 "
            pdb=" N   ILE J 487 "
     model   vdw
     0.463 3.200
  nonbonded pdb=" CE1 HIS H  31 "
            pdb=" CA  ILE J 487 "
     model   vdw
     0.862 3.690
  nonbonded pdb=" CB  ALA H  34 "
            pdb=" CZ2 TRP J 484 "
     model   vdw
     0.934 3.760
  nonbonded pdb=" CA  ALA H  34 "
            pdb=" CH2 TRP J 484 "
     model   vdw
     1.025 3.770
  nonbonded pdb=" CE1 HIS H  31 "
            pdb=" N   ILE J 487 "
     model   vdw
     1.048 3.340
  ... (remaining 150710 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'G' and resid 9 through 173)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     15.830
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
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      :  0.008   0.242  17437  Z= 0.477
  Angle     :  1.130  14.570  23579  Z= 0.691
  Chirality :  0.064   0.414   2650
  Planarity :  0.006   0.076   3009
  Dihedral  : 15.939  89.102   6469
  Min Nonbonded Distance : 0.463

Molprobity Statistics.
  All-atom Clashscore : 43.24
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 11.91 %
    Favored  : 87.85 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  :  2.52 %
    Favored  : 92.82 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.17), residues: 2082
  helix: -0.89 (0.15), residues: 1038
  sheet: -1.65 (0.34), residues: 226
  loop : -2.49 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.038   0.002   ARG H 128 
 TYR   0.041   0.003   TYR J 253 
 PHE   0.037   0.004   PHE F 133 
 TRP   0.030   0.003   TRP A 147 
 HIS   0.017   0.003   HIS F 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00782 (17436)
  covalent geometry    : angle       1.12970 (23579)
  hydrogen bonds       : bond        0.16881 (  899)
  hydrogen bonds       : angle       7.48392 ( 2634)
  Misc. bond           : bond        0.24234 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 198
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.6079 (mmt) cc_final: 0.5845 (mmt)
REVERT: B   59 MET cc_start: 0.8492 (pmm) cc_final: 0.8036 (pmm)
REVERT: D    1 MET cc_start: 0.7074 (tpp) cc_final: 0.6868 (tpt)
REVERT: F  191 MET cc_start: -0.0898 (mtm) cc_final: -0.3024 (ttp)
REVERT: G   49 MET cc_start: 0.8085 (mmt) cc_final: 0.7855 (mmm)
REVERT: H    1 MET cc_start: 0.4687 (tpt) cc_final: 0.2849 (mtt)
REVERT: I  364 TYR cc_start: -0.2592 (OUTLIER) cc_final: -0.3183 (t80)
REVERT: I  436 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.5600 (t80)
REVERT: I  437 MET cc_start: 0.1210 (OUTLIER) cc_final: 0.0711 (ttt)
REVERT: I  501 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5576 (mmpt)
REVERT: I  502 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6839 (mm)
REVERT: I  507 THR cc_start: 0.7383 (p) cc_final: 0.6909 (t)
REVERT: I  508 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6203 (mtt-85)
REVERT: I  514 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7118 (tmm)
REVERT: J  268 GLU cc_start: 0.8756 (mp0) cc_final: 0.8344 (mm-30)
REVERT: J  436 MET cc_start: 0.9233 (tmm) cc_final: 0.8928 (tmm)
  outliers start: 87
  outliers final: 14
  residues processed: 269
  average time/residue: 0.1792
  time to fit residues: 66.3485
Evaluate side-chains
  138 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  364 TYR
Chi-restraints excluded: chain I residue  367 ARG
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  373 ILE
Chi-restraints excluded: chain I residue  429 ARG
Chi-restraints excluded: chain I residue  436 PHE
Chi-restraints excluded: chain I residue  437 MET
Chi-restraints excluded: chain I residue  448 TYR
Chi-restraints excluded: chain I residue  456 ASN
Chi-restraints excluded: chain I residue  480 THR
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain I residue  501 LYS
Chi-restraints excluded: chain I residue  502 LEU
Chi-restraints excluded: chain I residue  508 ARG
Chi-restraints excluded: chain I residue  514 MET
Chi-restraints excluded: chain I residue  515 GLU
Chi-restraints excluded: chain I residue  517 LEU
Chi-restraints excluded: chain I residue  526 VAL
Chi-restraints excluded: chain I residue  537 GLU
Chi-restraints excluded: chain I residue  594 VAL
Chi-restraints excluded: chain J residue  447 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 194 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   chunk 200 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 GLN
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 ASN
C  22 ASN
D  52 ASN
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  27 GLN
** G  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  93 ASN
I 375 HIS
I 427 GLN
I 561 HIS
** J  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  45 GLN
J 129 ASN
J 144 GLN
** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.055884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.040998 restraints weight = 236025.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.040361 restraints weight = 173902.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.040742 restraints weight = 136684.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.040939 restraints weight = 113852.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.041193 restraints weight = 101326.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100  17437  Z= 0.228
  Angle     :  0.852  10.882  23579  Z= 0.448
  Chirality :  0.050   0.508   2650
  Planarity :  0.006   0.075   3009
  Dihedral  :  7.937  81.471   2355
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 30.34
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.41 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.89 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.17), residues: 2082
  helix: -0.44 (0.14), residues: 1072
  sheet: -1.52 (0.34), residues: 230
  loop : -2.33 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG J 448 
 TYR   0.025   0.003   TYR D 180 
 PHE   0.038   0.003   PHE D 110 
 TRP   0.052   0.003   TRP J 484 
 HIS   0.019   0.002   HIS H  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 (17436)
  covalent geometry    : angle       0.85211 (23579)
  hydrogen bonds       : bond        0.05626 (  899)
  hydrogen bonds       : angle       5.90996 ( 2634)
  Misc. bond           : bond        0.02193 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 133
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.8290 (pm20) cc_final: 0.7880 (tm-30)
REVERT: B   48 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7374 (pt0)
REVERT: B   59 MET cc_start: 0.8462 (pmm) cc_final: 0.8259 (pmm)
REVERT: D    1 MET cc_start: 0.7350 (tpp) cc_final: 0.7052 (tpt)
REVERT: F  191 MET cc_start: 0.2043 (mtm) cc_final: 0.1624 (mtt)
REVERT: G   49 MET cc_start: 0.8527 (mmt) cc_final: 0.8097 (mmt)
REVERT: H    1 MET cc_start: 0.5204 (tpt) cc_final: 0.4482 (mtt)
REVERT: H   31 HIS cc_start: 0.6532 (OUTLIER) cc_final: 0.5560 (t-170)
REVERT: I  437 MET cc_start: 0.0792 (OUTLIER) cc_final: 0.0527 (ttt)
REVERT: I  489 MET cc_start: 0.1861 (ttp) cc_final: 0.1576 (ttp)
REVERT: I  514 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7156 (ttt)
REVERT: I  517 LEU cc_start: 0.4258 (OUTLIER) cc_final: 0.3928 (mt)
REVERT: I  533 MET cc_start: 0.7048 (tpp) cc_final: 0.6701 (mtt)
REVERT: I  560 MET cc_start: 0.4784 (ttp) cc_final: 0.4552 (ttp)
REVERT: J    1 MET cc_start: 0.4017 (ttm) cc_final: 0.3686 (mmt)
REVERT: J    3 MET cc_start: 0.3234 (tpt) cc_final: 0.3007 (tpt)
REVERT: J  106 MET cc_start: 0.6353 (ppp) cc_final: 0.5931 (ppp)
REVERT: J  238 MET cc_start: 0.8318 (mmm) cc_final: 0.8092 (mmm)
REVERT: J  315 PHE cc_start: 0.7393 (t80) cc_final: 0.6931 (m-80)
REVERT: J  455 MET cc_start: 0.8694 (mtt) cc_final: 0.8029 (mtt)
REVERT: J  581 MET cc_start: 0.8099 (ppp) cc_final: 0.7559 (ppp)
  outliers start: 36
  outliers final: 14
  residues processed: 162
  average time/residue: 0.1444
  time to fit residues: 34.8916
Evaluate side-chains
  127 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain B residue   48 GLU
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain H residue    8 ILE
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   31 HIS
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  437 MET
Chi-restraints excluded: chain I residue  473 LEU
Chi-restraints excluded: chain I residue  493 ILE
Chi-restraints excluded: chain I residue  508 ARG
Chi-restraints excluded: chain I residue  514 MET
Chi-restraints excluded: chain I residue  517 LEU
Chi-restraints excluded: chain I residue  561 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 138 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 154 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9980
   chunk 142 optimal weight:    7.9990
   chunk 89 optimal weight:    7.9990
   chunk 137 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 GLN
A 152 GLN
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 ASN
** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  48 ASN
** G  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 338 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.055562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.040017 restraints weight = 240831.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.039808 restraints weight = 169650.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.039953 restraints weight = 142981.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.039960 restraints weight = 119149.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.039960 restraints weight = 117113.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  17437  Z= 0.184
  Angle     :  0.768  10.096  23579  Z= 0.399
  Chirality :  0.046   0.323   2650
  Planarity :  0.005   0.068   3009
  Dihedral  :  6.813  78.444   2317
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 27.97
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.60 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.84 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.18), residues: 2082
  helix: -0.17 (0.15), residues: 1070
  sheet: -1.44 (0.34), residues: 225
  loop : -2.22 (0.22), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG H  96 
 TYR   0.036   0.002   TYR D  34 
 PHE   0.031   0.002   PHE D 110 
 TRP   0.043   0.002   TRP J 484 
 HIS   0.015   0.002   HIS H  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (17436)
  covalent geometry    : angle       0.76826 (23579)
  hydrogen bonds       : bond        0.04846 (  899)
  hydrogen bonds       : angle       5.62983 ( 2634)
  Misc. bond           : bond        0.02054 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 120
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 MET cc_start: 0.6873 (ppp) cc_final: 0.6577 (ppp)
REVERT: A  171 GLU cc_start: 0.8278 (pm20) cc_final: 0.7895 (tm-30)
REVERT: B   45 LEU cc_start: 0.2116 (OUTLIER) cc_final: 0.1641 (pt)
REVERT: D    1 MET cc_start: 0.7487 (tpp) cc_final: 0.6538 (tpt)
REVERT: D   69 MET cc_start: 0.8066 (ptm) cc_final: 0.7850 (ptm)
REVERT: E  110 MET cc_start: 0.7293 (mmp) cc_final: 0.6456 (mmp)
REVERT: F  191 MET cc_start: 0.2957 (mtm) cc_final: 0.2632 (mtt)
REVERT: H    3 PHE cc_start: 0.7965 (m-10) cc_final: 0.7698 (m-10)
REVERT: H   31 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.5552 (t-90)
REVERT: H   74 ASN cc_start: 0.6620 (OUTLIER) cc_final: 0.6419 (m110)
REVERT: I  437 MET cc_start: 0.1221 (OUTLIER) cc_final: 0.0930 (ttt)
REVERT: I  470 MET cc_start: 0.5050 (mmm) cc_final: 0.4603 (mtt)
REVERT: I  533 MET cc_start: 0.6852 (tpp) cc_final: 0.6528 (mtt)
REVERT: J    1 MET cc_start: 0.3919 (ttm) cc_final: 0.3630 (mmt)
REVERT: J  106 MET cc_start: 0.6490 (ppp) cc_final: 0.6078 (ppp)
REVERT: J  315 PHE cc_start: 0.7544 (t80) cc_final: 0.7136 (m-80)
REVERT: J  455 MET cc_start: 0.8664 (mtt) cc_final: 0.8016 (mtt)
REVERT: J  544 MET cc_start: 0.8490 (ptt) cc_final: 0.8289 (mtm)
REVERT: J  581 MET cc_start: 0.8153 (ppp) cc_final: 0.7717 (ppp)
  outliers start: 59
  outliers final: 24
  residues processed: 168
  average time/residue: 0.1412
  time to fit residues: 35.2843
Evaluate side-chains
  135 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain C residue   73 TYR
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain G residue  143 VAL
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   31 HIS
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain H residue  102 LEU
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  437 MET
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain J residue  185 THR
Chi-restraints excluded: chain J residue  230 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 158 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 144 optimal weight:    0.9990
   chunk 173 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 103 optimal weight:    9.9990
   chunk 129 optimal weight:    7.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  42 GLN
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
B 152 ASN
** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 504 GLN
** J  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.054927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.039127 restraints weight = 243578.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.038992 restraints weight = 168235.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.039268 restraints weight = 132369.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.039487 restraints weight = 115398.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.039839 restraints weight = 107161.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.4042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  17437  Z= 0.192
  Angle     :  0.748   9.684  23579  Z= 0.394
  Chirality :  0.046   0.263   2650
  Planarity :  0.005   0.066   3009
  Dihedral  :  6.386  72.855   2308
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 28.44
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.36 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.45 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.18), residues: 2082
  helix: -0.05 (0.15), residues: 1071
  sheet: -1.56 (0.33), residues: 237
  loop : -2.18 (0.22), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG I 453 
 TYR   0.026   0.002   TYR D 180 
 PHE   0.028   0.002   PHE A 148 
 TRP   0.042   0.003   TRP J 484 
 HIS   0.011   0.002   HIS H  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (17436)
  covalent geometry    : angle       0.74754 (23579)
  hydrogen bonds       : bond        0.04586 (  899)
  hydrogen bonds       : angle       5.55774 ( 2634)
  Misc. bond           : bond        0.02066 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 109
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7187 (t0)
REVERT: A   52 MET cc_start: 0.7429 (ppp) cc_final: 0.7136 (ppp)
REVERT: B   45 LEU cc_start: 0.2020 (OUTLIER) cc_final: 0.1604 (pt)
REVERT: D   69 MET cc_start: 0.7887 (ptm) cc_final: 0.7612 (ptm)
REVERT: E  110 MET cc_start: 0.7514 (mmp) cc_final: 0.6967 (mmp)
REVERT: F  188 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8920 (p0)
REVERT: F  191 MET cc_start: 0.3137 (mtm) cc_final: 0.2595 (mtt)
REVERT: H    3 PHE cc_start: 0.7986 (m-10) cc_final: 0.7763 (m-10)
REVERT: H   31 HIS cc_start: 0.6532 (OUTLIER) cc_final: 0.5823 (t-90)
REVERT: H   74 ASN cc_start: 0.6613 (OUTLIER) cc_final: 0.6336 (m110)
REVERT: I  437 MET cc_start: 0.0865 (ppp) cc_final: 0.0609 (ttt)
REVERT: I  470 MET cc_start: 0.5005 (mmm) cc_final: 0.4575 (mtt)
REVERT: J  106 MET cc_start: 0.6274 (ppp) cc_final: 0.5862 (ppp)
REVERT: J  232 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8735 (mt)
REVERT: J  238 MET cc_start: 0.8426 (mmm) cc_final: 0.8219 (mmm)
REVERT: J  315 PHE cc_start: 0.7416 (t80) cc_final: 0.7043 (m-80)
REVERT: J  374 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8768 (mp10)
REVERT: J  455 MET cc_start: 0.8734 (mtt) cc_final: 0.8033 (mtt)
REVERT: J  581 MET cc_start: 0.8267 (ppp) cc_final: 0.7972 (ppp)
  outliers start: 66
  outliers final: 33
  residues processed: 167
  average time/residue: 0.1267
  time to fit residues: 33.3178
Evaluate side-chains
  144 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 104
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  115 GLU
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain C residue    2 THR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   73 TYR
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  188 ASP
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain H residue    5 ILE
Chi-restraints excluded: chain H residue    8 ILE
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   31 HIS
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue   74 ASN
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  493 ILE
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain I residue  495 CYS
Chi-restraints excluded: chain J residue  185 THR
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain J residue  232 LEU
Chi-restraints excluded: chain J residue  374 GLN
Chi-restraints excluded: chain J residue  414 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 135 optimal weight:    4.9990
   chunk 140 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0670
   chunk 46 optimal weight:    0.9990
   chunk 204 optimal weight:    0.8980
   chunk 171 optimal weight:    0.4980
   chunk 92 optimal weight:    5.9990
   chunk 176 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 106 optimal weight:    8.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN
A 145 GLN
B 152 ASN
C  99 GLN
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  33 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.055978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.041044 restraints weight = 235810.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.040960 restraints weight = 179250.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.041444 restraints weight = 132986.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.041791 restraints weight = 108351.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.042175 restraints weight = 96617.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  17437  Z= 0.147
  Angle     :  0.726  12.429  23579  Z= 0.373
  Chirality :  0.046   0.366   2650
  Planarity :  0.004   0.064   3009
  Dihedral  :  6.078  68.754   2305
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 22.47
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.59 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.30 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.18), residues: 2082
  helix:  0.19 (0.15), residues: 1074
  sheet: -1.26 (0.36), residues: 207
  loop : -2.04 (0.22), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  75 
 TYR   0.020   0.002   TYR D 180 
 PHE   0.027   0.002   PHE J 230 
 TRP   0.040   0.002   TRP J 484 
 HIS   0.011   0.001   HIS H  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (17436)
  covalent geometry    : angle       0.72584 (23579)
  hydrogen bonds       : bond        0.04238 (  899)
  hydrogen bonds       : angle       5.28758 ( 2634)
  Misc. bond           : bond        0.01931 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 122
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 SER cc_start: 0.8222 (m) cc_final: 0.7984 (p)
REVERT: A   52 MET cc_start: 0.7081 (ppp) cc_final: 0.6845 (ppp)
REVERT: B   45 LEU cc_start: 0.2391 (OUTLIER) cc_final: 0.2074 (pt)
REVERT: C   56 ASP cc_start: 0.5365 (OUTLIER) cc_final: 0.5040 (m-30)
REVERT: D    1 MET cc_start: 0.7872 (tpt) cc_final: 0.7323 (tpt)
REVERT: D   69 MET cc_start: 0.7990 (ptm) cc_final: 0.7720 (ptm)
REVERT: E    5 TYR cc_start: 0.6124 (t80) cc_final: 0.5900 (t80)
REVERT: F  191 MET cc_start: 0.2365 (mtm) cc_final: 0.2109 (mtm)
REVERT: H    3 PHE cc_start: 0.8251 (m-10) cc_final: 0.7751 (m-10)
REVERT: H    4 CYS cc_start: 0.8905 (p) cc_final: 0.8122 (m)
REVERT: H   31 HIS cc_start: 0.6450 (OUTLIER) cc_final: 0.5753 (t-90)
REVERT: I  437 MET cc_start: 0.0870 (ppp) cc_final: 0.0556 (ttt)
REVERT: I  533 MET cc_start: 0.6681 (mtt) cc_final: 0.6238 (mtt)
REVERT: I  560 MET cc_start: 0.3432 (ttp) cc_final: 0.3071 (ttp)
REVERT: J    1 MET cc_start: 0.2516 (mmt) cc_final: 0.2072 (tpp)
REVERT: J  106 MET cc_start: 0.6476 (ppp) cc_final: 0.6091 (ppp)
REVERT: J  229 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8971 (mt0)
REVERT: J  232 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8616 (mt)
REVERT: J  315 PHE cc_start: 0.7478 (t80) cc_final: 0.7069 (m-80)
REVERT: J  455 MET cc_start: 0.8678 (mtt) cc_final: 0.8070 (mtt)
  outliers start: 63
  outliers final: 28
  residues processed: 175
  average time/residue: 0.1243
  time to fit residues: 34.1707
Evaluate side-chains
  156 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain C residue    2 THR
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 TYR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain G residue  143 VAL
Chi-restraints excluded: chain G residue  152 LEU
Chi-restraints excluded: chain H residue    5 ILE
Chi-restraints excluded: chain H residue    8 ILE
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   31 HIS
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  493 ILE
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain I residue  495 CYS
Chi-restraints excluded: chain J residue  185 THR
Chi-restraints excluded: chain J residue  229 GLN
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain J residue  232 LEU
Chi-restraints excluded: chain J residue  374 GLN
Chi-restraints excluded: chain J residue  414 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 188 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 177 optimal weight:    1.9990
   chunk 199 optimal weight:    4.9990
   chunk 150 optimal weight:   10.0000
   chunk 141 optimal weight:    6.9990
   chunk 129 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN
C  99 GLN
D 208 GLN
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.054132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 98)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.036891 restraints weight = 244455.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.037427 restraints weight = 177308.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.037640 restraints weight = 139363.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.037810 restraints weight = 122077.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.037810 restraints weight = 112310.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.4760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  17437  Z= 0.207
  Angle     :  0.784  14.703  23579  Z= 0.402
  Chirality :  0.046   0.235   2650
  Planarity :  0.006   0.081   3009
  Dihedral  :  6.119  60.044   2305
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 29.14
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.31 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.43 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.18), residues: 2082
  helix:  0.24 (0.15), residues: 1067
  sheet: -1.53 (0.35), residues: 212
  loop : -2.10 (0.21), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 194 
 TYR   0.025   0.002   TYR D 180 
 PHE   0.025   0.002   PHE A 148 
 TRP   0.040   0.002   TRP J 484 
 HIS   0.009   0.002   HIS H  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (17436)
  covalent geometry    : angle       0.78435 (23579)
  hydrogen bonds       : bond        0.04410 (  899)
  hydrogen bonds       : angle       5.43570 ( 2634)
  Misc. bond           : bond        0.01922 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 122
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.4961 (mmt) cc_final: 0.4733 (mmt)
REVERT: A   32 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7298 (t0)
REVERT: A   52 MET cc_start: 0.7339 (ppp) cc_final: 0.7099 (ppp)
REVERT: B   17 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5065 (p90)
REVERT: B   45 LEU cc_start: 0.2975 (OUTLIER) cc_final: 0.2613 (pt)
REVERT: C   56 ASP cc_start: 0.5576 (OUTLIER) cc_final: 0.5244 (m-30)
REVERT: D    1 MET cc_start: 0.7686 (tpt) cc_final: 0.7216 (tpt)
REVERT: D   69 MET cc_start: 0.8044 (ptm) cc_final: 0.7778 (ptm)
REVERT: F  113 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8465 (m170)
REVERT: G  115 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7077 (mm)
REVERT: H    3 PHE cc_start: 0.8327 (m-10) cc_final: 0.8009 (m-10)
REVERT: H    5 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8383 (pt)
REVERT: H  110 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7087 (mm)
REVERT: I  437 MET cc_start: 0.0800 (ppp) cc_final: 0.0493 (ttt)
REVERT: I  513 SER cc_start: 0.1015 (OUTLIER) cc_final: 0.0787 (p)
REVERT: J    1 MET cc_start: 0.2906 (mmt) cc_final: 0.2325 (tpp)
REVERT: J  103 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7203 (m-10)
REVERT: J  106 MET cc_start: 0.6670 (ppp) cc_final: 0.6313 (ppp)
REVERT: J  229 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8909 (mp10)
REVERT: J  232 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8792 (mt)
REVERT: J  315 PHE cc_start: 0.7356 (t80) cc_final: 0.7010 (m-80)
  outliers start: 65
  outliers final: 38
  residues processed: 180
  average time/residue: 0.1191
  time to fit residues: 34.2430
Evaluate side-chains
  165 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 115
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain C residue    2 THR
Chi-restraints excluded: chain C residue   10 ASP
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 TYR
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  143 VAL
Chi-restraints excluded: chain H residue    5 ILE
Chi-restraints excluded: chain H residue    8 ILE
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   31 HIS
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  110 ILE
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  493 ILE
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain I residue  495 CYS
Chi-restraints excluded: chain I residue  513 SER
Chi-restraints excluded: chain I residue  570 LEU
Chi-restraints excluded: chain J residue  103 PHE
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain J residue  185 THR
Chi-restraints excluded: chain J residue  229 GLN
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain J residue  232 LEU
Chi-restraints excluded: chain J residue  350 ILE
Chi-restraints excluded: chain J residue  374 GLN
Chi-restraints excluded: chain J residue  534 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 184 optimal weight:    0.8980
   chunk 103 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 137 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 146 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 163 optimal weight:    7.9990
   chunk 160 optimal weight:    5.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 561 HIS
** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.054412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.039174 restraints weight = 240606.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.038579 restraints weight = 171926.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.038992 restraints weight = 132631.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.039182 restraints weight = 110866.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.039335 restraints weight = 100937.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  17437  Z= 0.172
  Angle     :  0.754  11.869  23579  Z= 0.385
  Chirality :  0.045   0.215   2650
  Planarity :  0.005   0.060   3009
  Dihedral  :  6.023  53.316   2305
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 25.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.02 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.13 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.18), residues: 2082
  helix:  0.26 (0.15), residues: 1067
  sheet: -1.50 (0.34), residues: 222
  loop : -2.05 (0.22), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG J 696 
 TYR   0.024   0.002   TYR I 564 
 PHE   0.037   0.002   PHE I 553 
 TRP   0.040   0.002   TRP J 484 
 HIS   0.012   0.002   HIS I 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (17436)
  covalent geometry    : angle       0.75381 (23579)
  hydrogen bonds       : bond        0.04212 (  899)
  hydrogen bonds       : angle       5.36701 ( 2634)
  Misc. bond           : bond        0.01907 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 124
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7455 (t0)
REVERT: A   52 MET cc_start: 0.7362 (ppp) cc_final: 0.7155 (ppp)
REVERT: B   17 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5151 (p90)
REVERT: B   45 LEU cc_start: 0.2905 (OUTLIER) cc_final: 0.2569 (pt)
REVERT: C   56 ASP cc_start: 0.5641 (OUTLIER) cc_final: 0.5309 (m-30)
REVERT: D   69 MET cc_start: 0.8059 (ptm) cc_final: 0.7848 (ptm)
REVERT: E   98 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6834 (m-80)
REVERT: E  110 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6632 (mmp)
REVERT: F  113 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8409 (m170)
REVERT: G  115 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7162 (mm)
REVERT: H    3 PHE cc_start: 0.8293 (m-10) cc_final: 0.7854 (m-10)
REVERT: H    5 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8316 (pt)
REVERT: H  110 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7129 (mm)
REVERT: I  437 MET cc_start: 0.0771 (ppp) cc_final: 0.0529 (ttt)
REVERT: I  470 MET cc_start: 0.5115 (mmm) cc_final: 0.4788 (mtt)
REVERT: J    1 MET cc_start: 0.3476 (mmt) cc_final: 0.2915 (tpp)
REVERT: J  103 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.7107 (m-80)
REVERT: J  106 MET cc_start: 0.6514 (ppp) cc_final: 0.6153 (ppp)
REVERT: J  229 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8989 (mp10)
REVERT: J  232 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8807 (mt)
REVERT: J  238 MET cc_start: 0.8307 (mmm) cc_final: 0.7999 (mmm)
REVERT: J  315 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6894 (m-80)
REVERT: J  367 MET cc_start: 0.9693 (mmm) cc_final: 0.9438 (mpp)
REVERT: J  455 MET cc_start: 0.8773 (mtt) cc_final: 0.7886 (mtt)
  outliers start: 69
  outliers final: 40
  residues processed: 183
  average time/residue: 0.1169
  time to fit residues: 33.5685
Evaluate side-chains
  170 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 116
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 TYR
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  166 ILE
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain D residue  219 LYS
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain E residue  110 MET
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  143 VAL
Chi-restraints excluded: chain H residue    5 ILE
Chi-restraints excluded: chain H residue    8 ILE
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   31 HIS
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  110 ILE
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  493 ILE
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain I residue  495 CYS
Chi-restraints excluded: chain I residue  537 GLU
Chi-restraints excluded: chain I residue  561 HIS
Chi-restraints excluded: chain J residue   88 TRP
Chi-restraints excluded: chain J residue  103 PHE
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain J residue  185 THR
Chi-restraints excluded: chain J residue  229 GLN
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain J residue  232 LEU
Chi-restraints excluded: chain J residue  315 PHE
Chi-restraints excluded: chain J residue  350 ILE
Chi-restraints excluded: chain J residue  374 GLN
Chi-restraints excluded: chain J residue  534 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 186 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 136 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 179 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0170
   chunk 2 optimal weight:    5.9990
   chunk 168 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.1422

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 GLN
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 ASN
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 561 HIS
** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.054890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.040252 restraints weight = 236537.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.039939 restraints weight = 176688.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.040305 restraints weight = 129499.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.040737 restraints weight = 106287.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.040823 restraints weight = 92199.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  17437  Z= 0.150
  Angle     :  0.759  11.993  23579  Z= 0.384
  Chirality :  0.045   0.295   2650
  Planarity :  0.005   0.059   3009
  Dihedral  :  5.889  52.884   2305
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 24.25
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.07 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 21.39 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.18), residues: 2082
  helix:  0.33 (0.15), residues: 1071
  sheet: -1.48 (0.35), residues: 221
  loop : -1.99 (0.22), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 519 
 TYR   0.023   0.002   TYR I 564 
 PHE   0.044   0.002   PHE I 553 
 TRP   0.040   0.002   TRP J 484 
 HIS   0.021   0.002   HIS I 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (17436)
  covalent geometry    : angle       0.75879 (23579)
  hydrogen bonds       : bond        0.04055 (  899)
  hydrogen bonds       : angle       5.24423 ( 2634)
  Misc. bond           : bond        0.01862 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 124
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7505 (t0)
REVERT: A   52 MET cc_start: 0.7075 (ppp) cc_final: 0.6856 (ppp)
REVERT: B   17 TYR cc_start: 0.5485 (OUTLIER) cc_final: 0.4811 (p90)
REVERT: B   45 LEU cc_start: 0.2764 (OUTLIER) cc_final: 0.2487 (pt)
REVERT: C   56 ASP cc_start: 0.5622 (OUTLIER) cc_final: 0.5276 (m-30)
REVERT: D   69 MET cc_start: 0.8021 (ptm) cc_final: 0.7752 (ptm)
REVERT: D  204 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8803 (pt0)
REVERT: E   98 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6793 (m-80)
REVERT: F   93 LEU cc_start: 0.8987 (mt) cc_final: 0.8770 (mt)
REVERT: G  115 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7175 (mm)
REVERT: H    5 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8435 (pt)
REVERT: H  110 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7078 (mm)
REVERT: I  437 MET cc_start: 0.0751 (ppp) cc_final: 0.0549 (ttt)
REVERT: I  470 MET cc_start: 0.5049 (mmm) cc_final: 0.4687 (mtt)
REVERT: J    1 MET cc_start: 0.3700 (mmt) cc_final: 0.3188 (tpp)
REVERT: J  103 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.7001 (m-80)
REVERT: J  106 MET cc_start: 0.6442 (ppp) cc_final: 0.6110 (ppp)
REVERT: J  238 MET cc_start: 0.8332 (mmm) cc_final: 0.8073 (mmm)
REVERT: J  315 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6980 (m-80)
REVERT: J  455 MET cc_start: 0.8765 (mtt) cc_final: 0.7863 (mtt)
  outliers start: 63
  outliers final: 39
  residues processed: 178
  average time/residue: 0.1282
  time to fit residues: 35.8340
Evaluate side-chains
  167 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 118
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 TYR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  166 ILE
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain D residue  219 LYS
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  143 VAL
Chi-restraints excluded: chain G residue  152 LEU
Chi-restraints excluded: chain H residue    5 ILE
Chi-restraints excluded: chain H residue    8 ILE
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  110 ILE
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  493 ILE
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain I residue  495 CYS
Chi-restraints excluded: chain I residue  537 GLU
Chi-restraints excluded: chain I residue  561 HIS
Chi-restraints excluded: chain J residue   88 TRP
Chi-restraints excluded: chain J residue  103 PHE
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain J residue  185 THR
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain J residue  315 PHE
Chi-restraints excluded: chain J residue  350 ILE
Chi-restraints excluded: chain J residue  374 GLN
Chi-restraints excluded: chain J residue  534 LEU
Chi-restraints excluded: chain J residue  709 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 155 optimal weight:    8.9990
   chunk 118 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 187 optimal weight:    3.9990
   chunk 203 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 90 optimal weight:    0.4980
   chunk 30 optimal weight:    7.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN
** B  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 561 HIS
** J 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.054918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.040620 restraints weight = 235550.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.040854 restraints weight = 174475.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.040763 restraints weight = 127511.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.040640 restraints weight = 106958.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.040646 restraints weight = 92113.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.5337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  17437  Z= 0.151
  Angle     :  0.768  12.365  23579  Z= 0.390
  Chirality :  0.045   0.256   2650
  Planarity :  0.005   0.059   3009
  Dihedral  :  5.813  51.955   2305
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 24.14
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.73 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.77 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.18), residues: 2082
  helix:  0.33 (0.15), residues: 1071
  sheet: -1.46 (0.35), residues: 215
  loop : -1.97 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J 227 
 TYR   0.019   0.002   TYR I 564 
 PHE   0.054   0.002   PHE D 110 
 TRP   0.038   0.002   TRP J 484 
 HIS   0.016   0.002   HIS I 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (17436)
  covalent geometry    : angle       0.76788 (23579)
  hydrogen bonds       : bond        0.04075 (  899)
  hydrogen bonds       : angle       5.25689 ( 2634)
  Misc. bond           : bond        0.01834 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 123
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 SER cc_start: 0.8331 (m) cc_final: 0.8102 (p)
REVERT: A   32 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7487 (t0)
REVERT: B   17 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.4852 (p90)
REVERT: B   45 LEU cc_start: 0.3131 (OUTLIER) cc_final: 0.2885 (pt)
REVERT: B   59 MET cc_start: 0.8669 (pmm) cc_final: 0.8258 (pmm)
REVERT: C   56 ASP cc_start: 0.5637 (OUTLIER) cc_final: 0.5292 (m-30)
REVERT: D   69 MET cc_start: 0.8016 (ptm) cc_final: 0.7729 (ptm)
REVERT: D  204 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8902 (pt0)
REVERT: E   98 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6808 (m-80)
REVERT: F   93 LEU cc_start: 0.9000 (mt) cc_final: 0.8794 (mt)
REVERT: F  191 MET cc_start: 0.2370 (OUTLIER) cc_final: 0.1219 (mmt)
REVERT: G  115 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7219 (mm)
REVERT: H    5 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8452 (pt)
REVERT: H  110 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7064 (mm)
REVERT: I  470 MET cc_start: 0.4945 (mmm) cc_final: 0.4596 (mtt)
REVERT: J    1 MET cc_start: 0.3523 (mmt) cc_final: 0.3037 (tpp)
REVERT: J  106 MET cc_start: 0.6491 (ppp) cc_final: 0.6137 (ppp)
REVERT: J  238 MET cc_start: 0.8393 (mmm) cc_final: 0.8091 (mmm)
REVERT: J  315 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6991 (m-80)
REVERT: J  367 MET cc_start: 0.9675 (mmm) cc_final: 0.9442 (mpp)
REVERT: J  455 MET cc_start: 0.8750 (mtt) cc_final: 0.7895 (mtt)
  outliers start: 62
  outliers final: 41
  residues processed: 177
  average time/residue: 0.1214
  time to fit residues: 33.8788
Evaluate side-chains
  165 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 114
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 TYR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  166 ILE
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain D residue  219 LYS
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  191 MET
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  143 VAL
Chi-restraints excluded: chain G residue  152 LEU
Chi-restraints excluded: chain H residue    5 ILE
Chi-restraints excluded: chain H residue    8 ILE
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   31 HIS
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  110 ILE
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  493 ILE
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain I residue  495 CYS
Chi-restraints excluded: chain I residue  548 GLN
Chi-restraints excluded: chain I residue  561 HIS
Chi-restraints excluded: chain I residue  570 LEU
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain J residue  185 THR
Chi-restraints excluded: chain J residue  315 PHE
Chi-restraints excluded: chain J residue  350 ILE
Chi-restraints excluded: chain J residue  354 LYS
Chi-restraints excluded: chain J residue  374 GLN
Chi-restraints excluded: chain J residue  534 LEU
Chi-restraints excluded: chain J residue  709 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 92 optimal weight:    0.0470
   chunk 110 optimal weight:    6.9990
   chunk 186 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 163 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 60 optimal weight:    9.9990
   chunk 88 optimal weight:    0.7980
   chunk 108 optimal weight:    7.9990
   chunk 188 optimal weight:    5.9990
   chunk 164 optimal weight:    4.9990
   overall best weight:    2.3684

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 561 HIS
J  94 HIS
** J 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.054218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.039618 restraints weight = 240915.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.039189 restraints weight = 174853.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.039673 restraints weight = 137173.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.040101 restraints weight = 105803.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.040101 restraints weight = 93204.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.5516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  17437  Z= 0.180
  Angle     :  0.807  12.670  23579  Z= 0.413
  Chirality :  0.047   0.273   2650
  Planarity :  0.005   0.058   3009
  Dihedral  :  5.879  50.609   2305
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 26.53
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.41 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 22.52 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.18), residues: 2082
  helix:  0.26 (0.16), residues: 1069
  sheet: -1.56 (0.34), residues: 218
  loop : -2.03 (0.22), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG I 562 
 TYR   0.021   0.002   TYR D 180 
 PHE   0.049   0.002   PHE I 553 
 TRP   0.039   0.002   TRP J 484 
 HIS   0.014   0.002   HIS I 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (17436)
  covalent geometry    : angle       0.80743 (23579)
  hydrogen bonds       : bond        0.04206 (  899)
  hydrogen bonds       : angle       5.36342 ( 2634)
  Misc. bond           : bond        0.01853 (    1)

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

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

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4164 Ramachandran restraints generated.
    2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 104
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7621 (t0)
REVERT: A   52 MET cc_start: 0.6886 (ppp) cc_final: 0.6632 (ppp)
REVERT: B   17 TYR cc_start: 0.5636 (OUTLIER) cc_final: 0.3974 (p90)
REVERT: B   45 LEU cc_start: 0.3106 (OUTLIER) cc_final: 0.2869 (pt)
REVERT: B   59 MET cc_start: 0.8691 (pmm) cc_final: 0.8295 (pmm)
REVERT: C   56 ASP cc_start: 0.5717 (OUTLIER) cc_final: 0.5370 (m-30)
REVERT: D   69 MET cc_start: 0.7966 (ptm) cc_final: 0.7701 (ptm)
REVERT: D  204 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8913 (pt0)
REVERT: E   98 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6826 (m-80)
REVERT: F   93 LEU cc_start: 0.9018 (mt) cc_final: 0.8794 (mt)
REVERT: F  191 MET cc_start: 0.2725 (mtt) cc_final: 0.1184 (mmt)
REVERT: G  115 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7256 (mm)
REVERT: H    5 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8414 (pt)
REVERT: H  110 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7046 (mm)
REVERT: I  470 MET cc_start: 0.4971 (mmm) cc_final: 0.4608 (mtt)
REVERT: J    1 MET cc_start: 0.3715 (mmt) cc_final: 0.3224 (tpp)
REVERT: J  103 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7207 (m-80)
REVERT: J  106 MET cc_start: 0.6540 (ppp) cc_final: 0.6191 (ppp)
REVERT: J  238 MET cc_start: 0.8389 (mmm) cc_final: 0.8065 (mmm)
REVERT: J  315 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6985 (m-80)
REVERT: J  367 MET cc_start: 0.9681 (mmm) cc_final: 0.9452 (mpp)
REVERT: J  455 MET cc_start: 0.8753 (mtt) cc_final: 0.7908 (mtt)
  outliers start: 59
  outliers final: 43
  residues processed: 156
  average time/residue: 0.1069
  time to fit residues: 27.4282
Evaluate side-chains
  154 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 101
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   73 TYR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain D residue    2 ILE
Chi-restraints excluded: chain D residue   17 PHE
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  166 ILE
Chi-restraints excluded: chain D residue  177 TYR
Chi-restraints excluded: chain D residue  219 LYS
Chi-restraints excluded: chain E residue   85 VAL
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain G residue   61 THR
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain G residue  143 VAL
Chi-restraints excluded: chain H residue    5 ILE
Chi-restraints excluded: chain H residue    8 ILE
Chi-restraints excluded: chain H residue   30 TYR
Chi-restraints excluded: chain H residue   31 HIS
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  110 ILE
Chi-restraints excluded: chain I residue  369 LEU
Chi-restraints excluded: chain I residue  435 TYR
Chi-restraints excluded: chain I residue  476 PHE
Chi-restraints excluded: chain I residue  493 ILE
Chi-restraints excluded: chain I residue  494 VAL
Chi-restraints excluded: chain I residue  495 CYS
Chi-restraints excluded: chain I residue  548 GLN
Chi-restraints excluded: chain I residue  561 HIS
Chi-restraints excluded: chain I residue  570 LEU
Chi-restraints excluded: chain J residue  103 PHE
Chi-restraints excluded: chain J residue  136 THR
Chi-restraints excluded: chain J residue  185 THR
Chi-restraints excluded: chain J residue  230 PHE
Chi-restraints excluded: chain J residue  315 PHE
Chi-restraints excluded: chain J residue  350 ILE
Chi-restraints excluded: chain J residue  354 LYS
Chi-restraints excluded: chain J residue  374 GLN
Chi-restraints excluded: chain J residue  534 LEU
Chi-restraints excluded: chain J residue  709 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 205
   random chunks:
   chunk 116 optimal weight:    0.0970
   chunk 120 optimal weight:    0.7980
   chunk 110 optimal weight:    7.9990
   chunk 195 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 179 optimal weight:    5.9990
   chunk 198 optimal weight:    4.9990
   chunk 166 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 192 optimal weight:    3.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 561 HIS
** J 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.054255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.039228 restraints weight = 240683.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.038959 restraints weight = 173253.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.039483 restraints weight = 130892.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.039843 restraints weight = 105186.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.039986 restraints weight = 92179.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.5636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  17437  Z= 0.166
  Angle     :  0.790  12.976  23579  Z= 0.403
  Chirality :  0.046   0.270   2650
  Planarity :  0.005   0.058   3009
  Dihedral  :  5.867  49.704   2305
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 25.95
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.17 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 22.63 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    Cis-general     : 0.05 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.18), residues: 2082
  helix:  0.27 (0.16), residues: 1067
  sheet: -1.57 (0.34), residues: 219
  loop : -2.03 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG I 532 
 TYR   0.020   0.002   TYR D 180 
 PHE   0.039   0.002   PHE I 553 
 TRP   0.045   0.002   TRP J  88 
 HIS   0.020   0.002   HIS I 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (17436)
  covalent geometry    : angle       0.79045 (23579)
  hydrogen bonds       : bond        0.04158 (  899)
  hydrogen bonds       : angle       5.35171 ( 2634)
  Misc. bond           : bond        0.01858 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5374.75 seconds
wall clock time: 92 minutes 47.72 seconds (5567.72 seconds total)