Starting phenix.real_space_refine
on Fri Jul  3 20:27:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9p_36114/07_2026/8j9p_36114.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9p_36114/07_2026/8j9p_36114.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9p_36114/07_2026/8j9p_36114.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9p_36114/07_2026/8j9p_36114.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j9p_36114/07_2026/8j9p_36114.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9p_36114/07_2026/8j9p_36114.map"
  }
  resolution = 3.4
  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=   0.016
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: 6
    Type Number    sf(0)   Gaussians
     P      83      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C   10089      2.51       5
     N    2705      2.21       5
     O    3090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16013
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 3618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3618
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 25, 'TRANS': 422}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3529
          Classifications: {'peptide': 422}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 407}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 422
          Classifications: {'DNA': 13, 'RNA': 8}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 20}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen chiralities: 8
    Chain: "F"
      Number of atoms: 432
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 21, 432
          Classifications: {'DNA': 21}
          Link IDs: {'rna3p': 20}
    Chain: "C"
      Number of atoms: 3646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3646
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 25, 'TRANS': 425}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3531
          Classifications: {'peptide': 422}
          Link IDs: {'PTRANS': 14, 'TRANS': 407}
    Chain: "G"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 422
          Classifications: {'DNA': 13, 'RNA': 8}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 20}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen chiralities: 8
    Chain: "H"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 20, 411
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.09, per 1000 atoms: 0.26
  Number of scatterers: 16013
  At special positions: 0
  Unit cell: (113.4, 168, 137.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      44     16.00
     P      83     15.00
     Mg      2     11.99
     O    3090      8.00
     N    2705      7.00
     C   10089      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 770.9 milliseconds
  

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3310

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 23 sheets defined
      34.9% alpha, 14.3% beta
      26 base pairs and 58 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 17
      No H-bonds generated for 'chain 'A' and resid 15 through 17'
    Processing helix  chain 'A' and resid 22 through 30
    Processing helix  chain 'A' and resid 46 through 61
      removed outlier: 3.978A  pdb=" N   GLN A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.583A  pdb=" N   ASN A 107 " --> pdb=" O   TYR A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 132
      removed outlier: 3.548A  pdb=" N   PHE A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 214
      removed outlier: 3.670A  pdb=" N   LYS A 211 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 248 through 264
      removed outlier: 3.547A  pdb=" N   ALA A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.501A  pdb=" N   TYR A 346 " --> pdb=" O   ALA A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 375
    Processing helix  chain 'A' and resid 451 through 462
    Processing helix  chain 'A' and resid 477 through 492
      removed outlier: 3.606A  pdb=" N   ARG A 481 " --> pdb=" O   PRO A 477 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 483 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLU A 488 " --> pdb=" O   ASN A 484 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE A 489 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
      removed outlier: 4.006A  pdb=" N   TYR A 506 " --> pdb=" O   ALA A 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 29
    Processing helix  chain 'B' and resid 44 through 56
      removed outlier: 3.578A  pdb=" N   THR B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 89
      removed outlier: 3.647A  pdb=" N   HIS B  87 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN B  89 " --> pdb=" O   LYS B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 139
    Processing helix  chain 'B' and resid 151 through 156
      removed outlier: 3.945A  pdb=" N   GLN B 155 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 203
      removed outlier: 3.582A  pdb=" N   THR B 202 " --> pdb=" O   ASP B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 224
      removed outlier: 3.548A  pdb=" N   ASP B 222 " --> pdb=" O   TRP B 219 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   PHE B 223 " --> pdb=" O   GLU B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 248
    Processing helix  chain 'B' and resid 257 through 278
    Processing helix  chain 'B' and resid 300 through 304
      removed outlier: 3.668A  pdb=" N   ASP B 303 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 366
    Processing helix  chain 'B' and resid 369 through 384
    Processing helix  chain 'C' and resid 15 through 17
      No H-bonds generated for 'chain 'C' and resid 15 through 17'
    Processing helix  chain 'C' and resid 22 through 30
    Processing helix  chain 'C' and resid 46 through 60
    Processing helix  chain 'C' and resid 77 through 82
    Processing helix  chain 'C' and resid 100 through 108
      removed outlier: 3.759A  pdb=" N   TYR C 104 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   PHE C 106 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA C 108 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 132
      removed outlier: 3.722A  pdb=" N   ARG C 113 " --> pdb=" O   SER C 109 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   PHE C 121 " --> pdb=" O   LEU C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 214
    Processing helix  chain 'C' and resid 225 through 230
    Processing helix  chain 'C' and resid 248 through 265
      removed outlier: 3.522A  pdb=" N   GLY C 265 " --> pdb=" O   TYR C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 331 through 351
      removed outlier: 4.062A  pdb=" N   LYS C 336 " --> pdb=" O   PRO C 332 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ALA C 337 " --> pdb=" O   LYS C 333 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR C 346 " --> pdb=" O   ALA C 342 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 375
      removed outlier: 3.620A  pdb=" N   TRP C 370 " --> pdb=" O   ASN C 366 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE C 373 " --> pdb=" O   GLU C 369 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN C 374 " --> pdb=" O   TRP C 370 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLU C 375 " --> pdb=" O   ASN C 371 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 451 through 462
    Processing helix  chain 'C' and resid 463 through 465
      No H-bonds generated for 'chain 'C' and resid 463 through 465'
    Processing helix  chain 'C' and resid 477 through 493
      removed outlier: 4.071A  pdb=" N   ALA C 483 " --> pdb=" O   THR C 479 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASN C 484 " --> pdb=" O   LEU C 480 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLU C 488 " --> pdb=" O   ASN C 484 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ILE C 489 " --> pdb=" O   LYS C 485 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   SER C 493 " --> pdb=" O   ILE C 489 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 28
      removed outlier: 3.699A  pdb=" N   LEU D  21 " --> pdb=" O   PHE D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 52
    Processing helix  chain 'D' and resid 65 through 69
      removed outlier: 3.923A  pdb=" N   GLY D  68 " --> pdb=" O   SER D  65 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ASN D  69 " --> pdb=" O   THR D  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 65 through 69'
    Processing helix  chain 'D' and resid 71 through 89
      removed outlier: 3.845A  pdb=" N   LEU D  75 " --> pdb=" O   ARG D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 115
      removed outlier: 3.564A  pdb=" N   ARG D 114 " --> pdb=" O   GLU D 111 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU D 115 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 111 through 115'
    Processing helix  chain 'D' and resid 123 through 138
      removed outlier: 3.511A  pdb=" N   GLY D 127 " --> pdb=" O   SER D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 146 through 158
      removed outlier: 4.074A  pdb=" N   SER D 150 " --> pdb=" O   ASP D 146 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 248
    Processing helix  chain 'D' and resid 257 through 277
      removed outlier: 3.731A  pdb=" N   CYS D 261 " --> pdb=" O   ARG D 257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 280
      No H-bonds generated for 'chain 'D' and resid 278 through 280'
    Processing helix  chain 'D' and resid 300 through 304
    Processing helix  chain 'D' and resid 353 through 366
    Processing helix  chain 'D' and resid 369 through 385
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6
      removed outlier: 5.429A  pdb=" N   ILE A 443 " --> pdb=" O   THR A 389 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   THR A 389 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   ILE A 445 " --> pdb=" O   THR A 387 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   THR A 387 " --> pdb=" O   ILE A 445 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS A 447 " --> pdb=" O   GLY A 385 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 384 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   CYS A 279 " --> pdb=" O   PHE A 358 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   HIS A 360 " --> pdb=" O   CYS A 279 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU A 281 " --> pdb=" O   HIS A 360 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13
    Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 95
      removed outlier: 3.634A  pdb=" N   LYS A  94 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLY A  45 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   GLY A  42 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   ILE A 142 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL A  44 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285
      removed outlier: 3.766A  pdb=" N   VAL A 284 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ALA A 300 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 306
    Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398
    Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 426
      removed outlier: 3.563A  pdb=" N   SER A 431 " --> pdb=" O   VAL A 426 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 64
      removed outlier: 3.842A  pdb=" N   ALA B  98 " --> pdb=" O   ILE B 118 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 177
    Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 177
    Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 210
    Processing sheet with id=AB3, first strand: chain 'B' and resid 390 through 394
    Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 6
      removed outlier: 6.875A  pdb=" N   GLY C 385 " --> pdb=" O   ASN C 446 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE C 358 " --> pdb=" O   CYS C 279 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 12 through 13
    Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 95
      removed outlier: 3.610A  pdb=" N   LYS C  94 " --> pdb=" O   VAL C  43 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY C  45 " --> pdb=" O   LYS C  94 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY C  42 " --> pdb=" O   PHE C 140 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   ILE C 142 " --> pdb=" O   GLY C  42 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL C  44 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   TRP C 139 " --> pdb=" O   GLN C 222 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   LEU C 224 " --> pdb=" O   TRP C 139 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   VAL C 141 " --> pdb=" O   LEU C 224 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 300 through 306
    Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 398
      removed outlier: 4.678A  pdb=" N   GLU D 169 " --> pdb=" O   GLY D 412 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLY D 412 " --> pdb=" O   GLU D 169 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 425 through 426
    Processing sheet with id=AC1, first strand: chain 'D' and resid 63 through 64
    Processing sheet with id=AC2, first strand: chain 'D' and resid 214 through 216
    Processing sheet with id=AC3, first strand: chain 'D' and resid 283 through 285
    Processing sheet with id=AC4, first strand: chain 'D' and resid 311 through 314
    Processing sheet with id=AC5, first strand: chain 'D' and resid 390 through 394

    517 hydrogen bonds defined for protein.
    1443 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      65 hydrogen bonds
      128 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      58 stacking parallelities
  Total time for adding SS restraints: 2.70

  Time building geometry restraints manager: 1.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 4149
        1.33 -     1.45: 3466
        1.45 -     1.57: 8732
        1.57 -     1.69: 162
        1.69 -     1.81: 68
  Bond restraints: 16577
  Sorted by residual:
  bond pdb=" C3'  DA F  14 "
       pdb=" C2'  DA F  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.12e+01
  bond pdb=" C3'  DA H  14 "
       pdb=" C2'  DA H  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  bond pdb=" C3'A DT F  13 "
       pdb=" C2'A DT F  13 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.08e+01
  bond pdb=" C3'  DA H   7 "
       pdb=" C2'  DA H   7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.04e+01
  bond pdb=" N9   DA F   3 "
       pdb=" C4   DA F   3 "
    ideal  model  delta    sigma   weight residual
    1.374  1.393 -0.019 6.00e-03 2.78e+04 9.69e+00
  ... (remaining 16572 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 22208
        1.91 -     3.81: 458
        3.81 -     5.72: 58
        5.72 -     7.62: 16
        7.62 -     9.53: 4
  Bond angle restraints: 22744
  Sorted by residual:
  angle pdb=" O4'   U G  17 "
        pdb=" C1'   U G  17 "
        pdb=" N1    U G  17 "
      ideal   model   delta    sigma   weight residual
     108.50  114.57   -6.07 7.00e-01 2.04e+00 7.53e+01
  angle pdb=" O5'   U G  21 "
        pdb=" C5'   U G  21 "
        pdb=" C4'   U G  21 "
      ideal   model   delta    sigma   weight residual
     109.40  115.93   -6.53 8.00e-01 1.56e+00 6.66e+01
  angle pdb=" O5'   U E  21 "
        pdb=" C5'   U E  21 "
        pdb=" C4'   U E  21 "
      ideal   model   delta    sigma   weight residual
     109.40  115.27   -5.87 8.00e-01 1.56e+00 5.39e+01
  angle pdb=" C2'   U E  15 "
        pdb=" C1'   U E  15 "
        pdb=" N1    U E  15 "
      ideal   model   delta    sigma   weight residual
     112.00  119.60   -7.60 1.10e+00 8.26e-01 4.77e+01
  angle pdb=" O4'   U E  17 "
        pdb=" C1'   U E  17 "
        pdb=" N1    U E  17 "
      ideal   model   delta    sigma   weight residual
     108.50  112.47   -3.97 7.00e-01 2.04e+00 3.21e+01
  ... (remaining 22739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.16: 8974
       29.16 -    58.31: 783
       58.31 -    87.47: 68
       87.47 -   116.62: 0
      116.62 -   145.78: 6
  Dihedral angle restraints: 9831
    sinusoidal: 4709
      harmonic: 5122
  Sorted by residual:
  dihedral pdb=" CA  ARG D 193 "
           pdb=" C   ARG D 193 "
           pdb=" N   LEU D 194 "
           pdb=" CA  LEU D 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.35  -23.65     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  ARG B 189 "
           pdb=" C   ARG B 189 "
           pdb=" N   TYR B 190 "
           pdb=" CA  TYR B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  TYR A 328 "
           pdb=" C   TYR A 328 "
           pdb=" N   HIS A 329 "
           pdb=" CA  HIS A 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.63  -20.37     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 9828 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 2000
       0.058 -    0.115: 409
       0.115 -    0.173: 40
       0.173 -    0.230: 4
       0.230 -    0.288: 3
  Chirality restraints: 2456
  Sorted by residual:
  chirality pdb=" CG  LEU D 227 "
            pdb=" CB  LEU D 227 "
            pdb=" CD1 LEU D 227 "
            pdb=" CD2 LEU D 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" C1'   U E   1 "
            pdb=" O4'   U E   1 "
            pdb=" C2'   U E   1 "
            pdb=" N1    U E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.19    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" C1'   U E  15 "
            pdb=" O4'   U E  15 "
            pdb=" C2'   U E  15 "
            pdb=" N1    U E  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.22    0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 2453 not shown)

  Planarity restraints: 2595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 318 "   -0.039 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO C 319 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO C 319 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 319 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 193 "    0.153 9.50e-02 1.11e+02   6.91e-02 3.54e+00
        pdb=" NE  ARG D 193 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 193 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 193 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 193 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F   4 "    0.001 2.00e-02 2.50e+03   1.25e-02 3.51e+00
        pdb=" N1   DC F   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DC F   4 "    0.029 2.00e-02 2.50e+03
        pdb=" O2   DC F   4 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3   DC F   4 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4   DC F   4 "    0.011 2.00e-02 2.50e+03
        pdb=" N4   DC F   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DC F   4 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DC F   4 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2592 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 188
        2.60 -     3.17: 13089
        3.17 -     3.75: 24642
        3.75 -     4.32: 31554
        4.32 -     4.90: 51641
  Nonbonded interactions: 121114
  Sorted by model distance:
  nonbonded pdb=" OP3   U G   1 "
            pdb="MG    MG G 101 "
     model   vdw
     2.020 2.170
  nonbonded pdb=" OP1   A G   3 "
            pdb="MG    MG G 101 "
     model   vdw
     2.089 2.170
  nonbonded pdb=" NE2 GLN A 302 "
            pdb=" O   THR A 479 "
     model   vdw
     2.150 3.120
  nonbonded pdb=" O4    U E  21 "
            pdb=" N7   DA F   3 "
     model   vdw
     2.154 2.496
  nonbonded pdb=" OD1 ASN A 307 "
            pdb=" N   GLY A 308 "
     model   vdw
     2.162 3.120
  ... (remaining 121109 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' and resid 1 through 507)
  selection = (chain 'C' and (resid 1 through 144 or resid 204 through 507))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and (resid 1 through 421 or (resid 422 and (name N or name CA or name \ 
 C or name O or name CB ))))
}
ncs_group {
  reference = chain 'E'
  selection = (chain 'G' and resid 1 through 21)
}
ncs_group {
  reference = (chain 'F' and resid 4 through 23)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.95 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     17.030
  Find NCS groups from input model:        0.280
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
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      :  0.003   0.047  16577  Z= 0.251
  Angle     :  0.653   9.528  22744  Z= 0.437
  Chirality :  0.046   0.288   2456
  Planarity :  0.004   0.069   2595
  Dihedral  : 19.679 145.777   6521
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 32.07 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.61 (0.20), residues: 1731
  helix:  0.74 (0.23), residues: 550
  sheet: -0.58 (0.32), residues: 307
  loop : -2.56 (0.18), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG D 193 
 TYR   0.019   0.001   TYR C 104 
 PHE   0.016   0.001   PHE D 273 
 TRP   0.021   0.001   TRP D  20 
 HIS   0.002   0.001   HIS D 320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.25 (16577)
  covalent geometry    : angle       0.65308 /  0.44 (22744)
  hydrogen bonds       : bond        0.14069 /  8.98 (  568)
  hydrogen bonds       : angle       5.44009 /  3.85 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.575 
Fit side-chains
REVERT: A  307 ASN cc_start: 0.7561 (t0) cc_final: 0.7329 (t0)
REVERT: C  247 LYS cc_start: 0.8419 (mptt) cc_final: 0.7995 (mmtt)
REVERT: D  219 TRP cc_start: 0.8151 (m100) cc_final: 0.7476 (m100)
  outliers start: 4
  outliers final: 3
  residues processed: 113
  average time/residue: 0.1247
  time to fit residues: 21.9570
Evaluate side-chains
  105 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain B residue  156 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 98 optimal weight:    0.3980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0670
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0470
   chunk 149 optimal weight:    0.0570
   overall best weight:    0.3134

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 295 GLN
A 296 ASN
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 ASN
** C  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS
C 205 GLN
C 295 GLN
C 296 ASN
C 302 GLN
D 405 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.097095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.074392 restraints weight = 54893.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 4.73
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.0701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  16577  Z= 0.128
  Angle     :  0.600  10.177  22744  Z= 0.329
  Chirality :  0.044   0.294   2456
  Planarity :  0.004   0.051   2595
  Dihedral  : 16.999 150.971   2904
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 29.18 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.62 (0.20), residues: 1731
  helix:  0.63 (0.23), residues: 561
  sheet: -0.53 (0.31), residues: 330
  loop : -2.61 (0.18), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 193 
 TYR   0.015   0.001   TYR C 104 
 PHE   0.015   0.001   PHE D 273 
 TRP   0.013   0.001   TRP D  20 
 HIS   0.006   0.001   HIS C 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.13 (16577)
  covalent geometry    : angle       0.59989 /  0.33 (22744)
  hydrogen bonds       : bond        0.04593 /  3.04 (  568)
  hydrogen bonds       : angle       4.65590 /  3.30 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 105
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A  307 ASN cc_start: 0.7626 (t0) cc_final: 0.7309 (t0)
REVERT: A  394 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8757 (tt)
REVERT: A  506 TYR cc_start: 0.8987 (m-80) cc_final: 0.8721 (m-80)
REVERT: C   74 MET cc_start: 0.6194 (tpp) cc_final: 0.5867 (ttm)
REVERT: C  111 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8728 (p-80)
REVERT: C  233 ASP cc_start: 0.8883 (t0) cc_final: 0.8473 (p0)
REVERT: C  243 ARG cc_start: 0.9195 (tpp80) cc_final: 0.8516 (mmm160)
REVERT: C  369 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8576 (pt0)
REVERT: C  432 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7819 (t)
REVERT: C  488 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8014 (pm20)
REVERT: C  501 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9022 (pp)
REVERT: D  219 TRP cc_start: 0.8011 (m100) cc_final: 0.7327 (m100)
REVERT: D  354 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7819 (mmtp)
  outliers start: 42
  outliers final: 14
  residues processed: 143
  average time/residue: 0.1183
  time to fit residues: 25.5837
Evaluate side-chains
  121 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  432 THR
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 LEU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  217 PHE
Chi-restraints excluded: chain D residue  297 LYS
Chi-restraints excluded: chain D residue  354 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 177 optimal weight:   10.0000
   chunk 105 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 141 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 296 ASN
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 357 GLN
** C  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.094405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.071820 restraints weight = 56765.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 4.75
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16577  Z= 0.205
  Angle     :  0.629   9.381  22744  Z= 0.343
  Chirality :  0.045   0.307   2456
  Planarity :  0.004   0.045   2595
  Dihedral  : 16.923 150.711   2897
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 28.41 %
    Favored  : 67.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.72 (0.20), residues: 1731
  helix:  0.60 (0.22), residues: 559
  sheet: -0.69 (0.30), residues: 339
  loop : -2.66 (0.19), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 193 
 TYR   0.023   0.001   TYR D 213 
 PHE   0.014   0.001   PHE D 273 
 TRP   0.019   0.001   TRP D 124 
 HIS   0.018   0.002   HIS C 111 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.21 (16577)
  covalent geometry    : angle       0.62927 /  0.34 (22744)
  hydrogen bonds       : bond        0.05179 /  3.41 (  568)
  hydrogen bonds       : angle       4.75381 /  3.38 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 99
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.5657 (p90)
REVERT: A  307 ASN cc_start: 0.7840 (t0) cc_final: 0.7470 (t0)
REVERT: A  462 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9031 (tt)
REVERT: A  506 TYR cc_start: 0.9055 (m-80) cc_final: 0.8754 (m-80)
REVERT: C  111 HIS cc_start: 0.9103 (m90) cc_final: 0.8730 (p-80)
REVERT: C  283 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9138 (mp)
REVERT: C  369 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8812 (pt0)
REVERT: C  388 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9017 (mp)
REVERT: C  432 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7544 (t)
REVERT: D  219 TRP cc_start: 0.8027 (m100) cc_final: 0.7322 (m100)
REVERT: D  354 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7898 (mmtp)
  outliers start: 68
  outliers final: 30
  residues processed: 156
  average time/residue: 0.1254
  time to fit residues: 29.7807
Evaluate side-chains
  131 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 94
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  432 THR
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  217 PHE
Chi-restraints excluded: chain D residue  225 HIS
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  418 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 138 optimal weight:    4.9990
   chunk 102 optimal weight:    0.8980
   chunk 54 optimal weight:   20.0000
   chunk 148 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 123 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 118 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 81 optimal weight:    4.9990
   chunk 142 optimal weight:    9.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  35 GLN
A 251 HIS
A 296 ASN
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 357 GLN
** C  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 430 GLN
D 340 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.092621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.069832 restraints weight = 55897.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 4.67
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (33 function evaluations)
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  16577  Z= 0.273
  Angle     :  0.681   9.712  22744  Z= 0.372
  Chirality :  0.047   0.342   2456
  Planarity :  0.004   0.050   2595
  Dihedral  : 17.027 151.903   2897
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.19 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 27.83 %
    Favored  : 66.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.95 (0.19), residues: 1731
  helix:  0.36 (0.22), residues: 567
  sheet: -0.85 (0.30), residues: 340
  loop : -2.78 (0.19), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 232 
 TYR   0.030   0.002   TYR D 213 
 PHE   0.019   0.002   PHE A 365 
 TRP   0.020   0.002   TRP D 124 
 HIS   0.009   0.001   HIS C  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00610 /  0.27 (16577)
  covalent geometry    : angle       0.68148 /  0.37 (22744)
  hydrogen bonds       : bond        0.05682 /  3.73 (  568)
  hydrogen bonds       : angle       4.93436 /  3.52 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 95
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.5930 (p90)
REVERT: A  275 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7693 (mtm-85)
REVERT: A  307 ASN cc_start: 0.8139 (t0) cc_final: 0.7760 (t0)
REVERT: A  462 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9060 (tt)
REVERT: B  181 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8631 (m-80)
REVERT: B  217 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.7949 (t80)
REVERT: C   37 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.5662 (p90)
REVERT: C  111 HIS cc_start: 0.9164 (m90) cc_final: 0.8798 (p-80)
REVERT: C  283 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9117 (mp)
REVERT: C  369 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8911 (pt0)
REVERT: C  388 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9032 (mp)
REVERT: C  488 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8094 (pm20)
REVERT: C  501 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9095 (pp)
REVERT: D  219 TRP cc_start: 0.8085 (m100) cc_final: 0.7429 (m100)
REVERT: D  354 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7960 (mmtp)
  outliers start: 86
  outliers final: 54
  residues processed: 169
  average time/residue: 0.1126
  time to fit residues: 29.6791
Evaluate side-chains
  157 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 91
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  275 ARG
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  181 PHE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  303 MET
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  217 PHE
Chi-restraints excluded: chain D residue  225 HIS
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  418 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 134 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 111 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 86 optimal weight:   10.0000
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 296 ASN
B 357 GLN
** C  67 HIS ** 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 = 0.3660 r_free = 0.3660 target = 0.094778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.072121 restraints weight = 55971.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 4.69
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (14 function evaluations)
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16577  Z= 0.136
  Angle     :  0.606   9.586  22744  Z= 0.330
  Chirality :  0.045   0.320   2456
  Planarity :  0.004   0.047   2595
  Dihedral  : 16.973 152.076   2897
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 29.18 %
    Favored  : 66.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.77 (0.20), residues: 1731
  helix:  0.60 (0.22), residues: 561
  sheet: -0.77 (0.30), residues: 316
  loop : -2.67 (0.19), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 201 
 TYR   0.020   0.001   TYR D 213 
 PHE   0.013   0.001   PHE A 206 
 TRP   0.017   0.001   TRP D 124 
 HIS   0.005   0.001   HIS C  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.14 (16577)
  covalent geometry    : angle       0.60591 /  0.33 (22744)
  hydrogen bonds       : bond        0.04517 /  2.96 (  568)
  hydrogen bonds       : angle       4.61077 /  3.29 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 99
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.5809 (p90)
REVERT: A  275 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7681 (mtm-85)
REVERT: A  296 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8358 (p0)
REVERT: A  307 ASN cc_start: 0.8276 (t0) cc_final: 0.7898 (t0)
REVERT: A  462 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9025 (tt)
REVERT: A  506 TYR cc_start: 0.8974 (m-80) cc_final: 0.8658 (m-80)
REVERT: B   92 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.5372 (pmm)
REVERT: B  217 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8081 (t80)
REVERT: B  296 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8179 (tp30)
REVERT: C   37 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.5853 (p90)
REVERT: C  111 HIS cc_start: 0.9099 (m90) cc_final: 0.8779 (p-80)
REVERT: C  222 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7898 (tp-100)
REVERT: C  302 GLN cc_start: 0.8514 (mp10) cc_final: 0.7786 (mp10)
REVERT: C  369 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8929 (pt0)
REVERT: C  388 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.9000 (mp)
REVERT: C  488 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8061 (pm20)
REVERT: C  501 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9038 (pp)
REVERT: D   60 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6941 (t80)
REVERT: D  219 TRP cc_start: 0.8026 (m100) cc_final: 0.7373 (m100)
REVERT: D  354 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7908 (mmtp)
REVERT: D  406 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8687 (mmtm)
  outliers start: 72
  outliers final: 43
  residues processed: 158
  average time/residue: 0.1239
  time to fit residues: 29.9038
Evaluate side-chains
  154 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 95
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  275 ARG
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  296 GLU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  405 ILE
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  217 PHE
Chi-restraints excluded: chain D residue  225 HIS
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  406 LYS
Chi-restraints excluded: chain D residue  418 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 164 optimal weight:    2.9990
   chunk 162 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 154 optimal weight:    0.6980
   chunk 89 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 86 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 296 ASN
** C  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.093250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.070664 restraints weight = 56619.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 4.70
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  16577  Z= 0.221
  Angle     :  0.653  11.251  22744  Z= 0.353
  Chirality :  0.046   0.317   2456
  Planarity :  0.004   0.049   2595
  Dihedral  : 16.998 152.703   2897
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 28.53 %
    Favored  : 66.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.81 (0.20), residues: 1731
  helix:  0.52 (0.22), residues: 562
  sheet: -0.77 (0.30), residues: 334
  loop : -2.72 (0.19), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 250 
 TYR   0.027   0.001   TYR D 213 
 PHE   0.022   0.001   PHE D  17 
 TRP   0.019   0.001   TRP D 124 
 HIS   0.007   0.001   HIS C  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00492 /  0.22 (16577)
  covalent geometry    : angle       0.65334 /  0.35 (22744)
  hydrogen bonds       : bond        0.05146 /  3.37 (  568)
  hydrogen bonds       : angle       4.76344 /  3.39 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 97
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.6241 (p90)
REVERT: A  275 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7690 (mtm-85)
REVERT: A  296 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8345 (p0)
REVERT: A  307 ASN cc_start: 0.8438 (t0) cc_final: 0.8021 (t0)
REVERT: A  432 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7371 (t)
REVERT: A  462 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9053 (tt)
REVERT: A  506 TYR cc_start: 0.9015 (m-80) cc_final: 0.8717 (m-80)
REVERT: B  217 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8195 (t80)
REVERT: B  296 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8207 (tp30)
REVERT: C   37 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.6101 (p90)
REVERT: C  111 HIS cc_start: 0.9123 (m90) cc_final: 0.8801 (p-80)
REVERT: C  369 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8908 (pt0)
REVERT: C  388 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9036 (mp)
REVERT: C  488 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8081 (pm20)
REVERT: C  501 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9069 (pp)
REVERT: D  219 TRP cc_start: 0.8012 (m100) cc_final: 0.7401 (m100)
REVERT: D  354 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7952 (mmtp)
REVERT: D  406 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8684 (mmtm)
  outliers start: 83
  outliers final: 57
  residues processed: 169
  average time/residue: 0.1152
  time to fit residues: 30.4265
Evaluate side-chains
  165 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 94
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  275 ARG
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  296 GLU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  405 ILE
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  217 PHE
Chi-restraints excluded: chain D residue  225 HIS
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  406 LYS
Chi-restraints excluded: chain D residue  418 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 135 optimal weight:    9.9990
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 128 optimal weight:    0.3980
   chunk 178 optimal weight:   10.0000
   chunk 94 optimal weight:    3.9990
   chunk 142 optimal weight:    1.9990
   chunk 87 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.8788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 296 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.093005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.070454 restraints weight = 55615.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 4.69
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16577  Z= 0.199
  Angle     :  0.645  11.697  22744  Z= 0.349
  Chirality :  0.046   0.320   2456
  Planarity :  0.004   0.048   2595
  Dihedral  : 17.011 153.204   2897
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 28.47 %
    Favored  : 65.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.85 (0.20), residues: 1731
  helix:  0.52 (0.22), residues: 562
  sheet: -0.80 (0.31), residues: 310
  loop : -2.71 (0.19), residues: 859

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 201 
 TYR   0.026   0.001   TYR D 213 
 PHE   0.013   0.001   PHE A 365 
 TRP   0.019   0.001   TRP D 124 
 HIS   0.007   0.001   HIS C  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.20 (16577)
  covalent geometry    : angle       0.64454 /  0.35 (22744)
  hydrogen bonds       : bond        0.05004 /  3.27 (  568)
  hydrogen bonds       : angle       4.73009 /  3.37 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 97
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.6343 (p90)
REVERT: A  275 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7666 (mtm-85)
REVERT: A  296 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8269 (p0)
REVERT: A  307 ASN cc_start: 0.8488 (t0) cc_final: 0.8102 (t0)
REVERT: A  462 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9055 (tt)
REVERT: A  506 TYR cc_start: 0.9017 (m-80) cc_final: 0.8730 (m-80)
REVERT: B   92 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.5387 (pmm)
REVERT: B  217 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8134 (t80)
REVERT: B  296 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8174 (tp30)
REVERT: C   37 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.6326 (p90)
REVERT: C  111 HIS cc_start: 0.9089 (m90) cc_final: 0.8790 (p-80)
REVERT: C  222 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7866 (tp-100)
REVERT: C  369 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8900 (pt0)
REVERT: C  388 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.9040 (mp)
REVERT: C  488 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8093 (pm20)
REVERT: C  501 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9068 (pp)
REVERT: D  219 TRP cc_start: 0.8025 (m100) cc_final: 0.7374 (m100)
REVERT: D  354 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7953 (mmtp)
REVERT: D  406 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8684 (mmtm)
  outliers start: 89
  outliers final: 59
  residues processed: 174
  average time/residue: 0.1154
  time to fit residues: 31.2093
Evaluate side-chains
  167 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 93
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  275 ARG
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  296 GLU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  222 GLN
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  179 ILE
Chi-restraints excluded: chain D residue  225 HIS
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  406 LYS
Chi-restraints excluded: chain D residue  418 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 133 optimal weight:    0.5980
   chunk 139 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 167 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   chunk 180 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 296 ASN
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 357 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.094791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.072253 restraints weight = 55852.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 4.73
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16577  Z= 0.127
  Angle     :  0.609   9.598  22744  Z= 0.331
  Chirality :  0.045   0.323   2456
  Planarity :  0.004   0.045   2595
  Dihedral  : 16.958 153.416   2897
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.95 %
    Favored  : 65.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.72 (0.20), residues: 1731
  helix:  0.57 (0.22), residues: 568
  sheet: -0.73 (0.30), residues: 310
  loop : -2.60 (0.19), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 283 
 TYR   0.018   0.001   TYR D 213 
 PHE   0.014   0.001   PHE D  17 
 TRP   0.016   0.001   TRP D 124 
 HIS   0.004   0.001   HIS C  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.13 (16577)
  covalent geometry    : angle       0.60921 /  0.33 (22744)
  hydrogen bonds       : bond        0.04219 /  2.75 (  568)
  hydrogen bonds       : angle       4.52810 /  3.23 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 93
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.6089 (p90)
REVERT: A  275 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7661 (mtm-85)
REVERT: A  307 ASN cc_start: 0.8585 (t0) cc_final: 0.8255 (t0)
REVERT: A  462 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9046 (tt)
REVERT: A  506 TYR cc_start: 0.8944 (m-80) cc_final: 0.8688 (m-80)
REVERT: B   92 MET cc_start: 0.5868 (OUTLIER) cc_final: 0.5590 (pmm)
REVERT: B  217 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8156 (t80)
REVERT: B  296 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (tp30)
REVERT: C   37 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.6173 (p90)
REVERT: C  111 HIS cc_start: 0.9053 (m90) cc_final: 0.8772 (p-80)
REVERT: C  302 GLN cc_start: 0.8523 (mp10) cc_final: 0.7844 (mp10)
REVERT: C  369 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8915 (pt0)
REVERT: C  388 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8999 (mp)
REVERT: C  488 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8039 (pm20)
REVERT: C  501 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9014 (pp)
REVERT: D  219 TRP cc_start: 0.8055 (m100) cc_final: 0.7412 (m100)
REVERT: D  354 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7921 (mmtp)
REVERT: D  406 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8673 (mmtm)
  outliers start: 71
  outliers final: 46
  residues processed: 153
  average time/residue: 0.1161
  time to fit residues: 27.5115
Evaluate side-chains
  151 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 92
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  275 ARG
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  296 GLU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  179 ILE
Chi-restraints excluded: chain D residue  225 HIS
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  406 LYS
Chi-restraints excluded: chain D residue  418 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 111 optimal weight:    0.7980
   chunk 151 optimal weight:    4.9990
   chunk 109 optimal weight:    0.6980
   chunk 136 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 138 optimal weight:    0.0040
   chunk 23 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 128 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9990
   overall best weight:    0.6594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 296 ASN
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 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 = 0.3669 r_free = 0.3669 target = 0.095109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.072517 restraints weight = 56093.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 4.73
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16577  Z= 0.126
  Angle     :  0.605   9.531  22744  Z= 0.326
  Chirality :  0.044   0.325   2456
  Planarity :  0.004   0.045   2595
  Dihedral  : 16.922 153.554   2897
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.15 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 30.40 %
    Favored  : 65.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 (0.20), residues: 1731
  helix:  0.62 (0.22), residues: 568
  sheet: -0.70 (0.30), residues: 318
  loop : -2.57 (0.19), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 102 
 TYR   0.017   0.001   TYR D 213 
 PHE   0.011   0.001   PHE A 206 
 TRP   0.014   0.001   TRP D 124 
 HIS   0.004   0.001   HIS C  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.13 (16577)
  covalent geometry    : angle       0.60522 /  0.33 (22744)
  hydrogen bonds       : bond        0.04071 /  2.66 (  568)
  hydrogen bonds       : angle       4.49058 /  3.21 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 93
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A    1 MET cc_start: 0.8507 (tpt) cc_final: 0.8210 (tpp)
REVERT: A   37 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.6080 (p90)
REVERT: A  275 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7674 (mtm-85)
REVERT: A  296 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8401 (p0)
REVERT: A  307 ASN cc_start: 0.8573 (t0) cc_final: 0.8260 (t0)
REVERT: A  462 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9051 (tt)
REVERT: A  506 TYR cc_start: 0.8937 (m-80) cc_final: 0.8690 (m-80)
REVERT: B   92 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.5531 (pmm)
REVERT: B  217 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8149 (t80)
REVERT: B  296 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8186 (tp30)
REVERT: C   37 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.6123 (p90)
REVERT: C  111 HIS cc_start: 0.9054 (m90) cc_final: 0.8774 (p-80)
REVERT: C  302 GLN cc_start: 0.8489 (mp10) cc_final: 0.7833 (mp10)
REVERT: C  369 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8880 (pt0)
REVERT: C  388 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8983 (mp)
REVERT: C  488 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8051 (pm20)
REVERT: C  501 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9009 (pp)
REVERT: D  219 TRP cc_start: 0.7983 (m100) cc_final: 0.7307 (m100)
REVERT: D  354 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7921 (mmtp)
  outliers start: 66
  outliers final: 46
  residues processed: 148
  average time/residue: 0.1226
  time to fit residues: 28.2302
Evaluate side-chains
  152 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 93
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  275 ARG
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  296 GLU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  418 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 120 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 128 optimal weight:    0.0980
   chunk 9 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 164 optimal weight:    0.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.094248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.071454 restraints weight = 55843.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 4.77
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16577  Z= 0.163
  Angle     :  0.618   9.853  22744  Z= 0.333
  Chirality :  0.045   0.324   2456
  Planarity :  0.004   0.046   2595
  Dihedral  : 16.935 153.939   2897
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.38 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 30.08 %
    Favored  : 65.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 (0.20), residues: 1731
  helix:  0.67 (0.22), residues: 562
  sheet: -0.76 (0.29), residues: 339
  loop : -2.59 (0.19), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 201 
 TYR   0.021   0.001   TYR D 213 
 PHE   0.015   0.001   PHE D  17 
 TRP   0.015   0.001   TRP D 124 
 HIS   0.011   0.001   HIS C  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.16 (16577)
  covalent geometry    : angle       0.61838 /  0.33 (22744)
  hydrogen bonds       : bond        0.04380 /  2.87 (  568)
  hydrogen bonds       : angle       4.55265 /  3.26 ( 1571)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 91
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A    1 MET cc_start: 0.8458 (tpt) cc_final: 0.8135 (tpp)
REVERT: A   37 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.6306 (p90)
REVERT: A  275 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7657 (mtm-85)
REVERT: A  365 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6982 (p90)
REVERT: A  462 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9061 (tt)
REVERT: A  506 TYR cc_start: 0.8970 (m-80) cc_final: 0.8709 (m-80)
REVERT: B   92 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.5579 (pmm)
REVERT: B  217 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8172 (t80)
REVERT: B  296 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8188 (tp30)
REVERT: C   37 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.6299 (p90)
REVERT: C  111 HIS cc_start: 0.9053 (m90) cc_final: 0.8773 (p90)
REVERT: C  302 GLN cc_start: 0.8505 (mp10) cc_final: 0.7871 (mp10)
REVERT: C  369 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8870 (pt0)
REVERT: C  388 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8998 (mp)
REVERT: C  488 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8040 (pm20)
REVERT: C  501 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9008 (pp)
REVERT: D  219 TRP cc_start: 0.8009 (m100) cc_final: 0.7330 (m100)
REVERT: D  354 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7923 (mmtp)
  outliers start: 66
  outliers final: 49
  residues processed: 146
  average time/residue: 0.1107
  time to fit residues: 25.2206
Evaluate side-chains
  151 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 89
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  275 ARG
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  292 LYS
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  365 PHE
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  458 ASP
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  296 GLU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   67 HIS
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  292 LYS
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  478 VAL
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   30 TYR
Chi-restraints excluded: chain D residue   58 CYS
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  418 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 122 optimal weight:    0.0870
   chunk 168 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 169 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 123 optimal weight:    0.8980
   chunk 126 optimal weight:    2.9990
   overall best weight:    0.7362

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.095360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.072809 restraints weight = 55516.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 4.68
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16577  Z= 0.124
  Angle     :  0.597  10.000  22744  Z= 0.322
  Chirality :  0.044   0.324   2456
  Planarity :  0.003   0.044   2595
  Dihedral  : 16.900 154.184   2897
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.39 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 29.88 %
    Favored  : 65.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -1.58 (0.20), residues: 1731
  helix:  0.68 (0.22), residues: 568
  sheet: -0.66 (0.30), residues: 321
  loop : -2.52 (0.19), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 209 
 TYR   0.016   0.001   TYR D 213 
 PHE   0.012   0.001   PHE A 206 
 TRP   0.016   0.001   TRP D 124 
 HIS   0.008   0.001   HIS C  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 (16577)
  covalent geometry    : angle       0.59719 /  0.32 (22744)
  hydrogen bonds       : bond        0.03937 /  2.58 (  568)
  hydrogen bonds       : angle       4.45205 /  3.19 ( 1571)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3064.39 seconds
wall clock time: 53 minutes 38.82 seconds (3218.82 seconds total)