Starting phenix.real_space_refine
on Sat Jun 14 11:03:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9p_36114/06_2025/8j9p_36114.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9p_36114/06_2025/8j9p_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j9p_36114/06_2025/8j9p_36114.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9p_36114/06_2025/8j9p_36114.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9p_36114/06_2025/8j9p_36114.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9p_36114/06_2025/8j9p_36114.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.54, per 1000 atoms: 0.60
  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: 3.59
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 4.91
  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: 5.29

  Time building geometry restraints manager: 4.27 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=" CB  LYS A  59 "
       pdb=" CG  LYS A  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 3.00e-02 1.11e+03 2.45e+00
  bond pdb=" CB  LYS A  62 "
       pdb=" CG  LYS A  62 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.55e+00
  bond pdb=" CB  ARG D 193 "
       pdb=" CG  ARG D 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.47e+00
  bond pdb=" C   TYR D 330 "
       pdb=" N   PRO D 331 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.20e-02 6.94e+03 1.35e+00
  bond pdb=" CG  LYS A  62 "
       pdb=" CD  LYS A  62 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.34e+00
  ... (remaining 16572 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 22276
        1.91 -     3.81: 391
        3.81 -     5.72: 59
        5.72 -     7.62: 14
        7.62 -     9.53: 4
  Bond angle restraints: 22744
  Sorted by residual:
  angle pdb=" CB  LYS A  59 "
        pdb=" CG  LYS A  59 "
        pdb=" CD  LYS A  59 "
      ideal   model   delta    sigma   weight residual
     111.30  120.39   -9.09 2.30e+00 1.89e-01 1.56e+01
  angle pdb=" CA  LYS A  59 "
        pdb=" CB  LYS A  59 "
        pdb=" CG  LYS A  59 "
      ideal   model   delta    sigma   weight residual
     114.10  121.55   -7.45 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" CB  LYS A  62 "
        pdb=" CG  LYS A  62 "
        pdb=" CD  LYS A  62 "
      ideal   model   delta    sigma   weight residual
     111.30  119.84   -8.54 2.30e+00 1.89e-01 1.38e+01
  angle pdb=" CA  LYS D  59 "
        pdb=" CB  LYS D  59 "
        pdb=" CG  LYS D  59 "
      ideal   model   delta    sigma   weight residual
     114.10  121.51   -7.41 2.00e+00 2.50e-01 1.37e+01
  angle pdb=" N   LEU B 310 "
        pdb=" CA  LEU B 310 "
        pdb=" C   LEU B 310 "
      ideal   model   delta    sigma   weight residual
     114.56  110.17    4.39 1.27e+00 6.20e-01 1.19e+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: 2070
       0.058 -    0.115: 345
       0.115 -    0.173: 35
       0.173 -    0.230: 3
       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      2.46    2.19    0.26 2.00e-01 2.50e+01 1.72e+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      2.46    2.22    0.24 2.00e-01 2.50e+01 1.41e+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:             3.670
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     38.310
  Find NCS groups from input model:        0.690
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
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= 0.125
  Angle     :  0.623   9.528  22744  Z= 0.323
  Chirality :  0.044   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 : 10.67
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (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
 TRP   0.021   0.001   TRP D  20 
 HIS   0.002   0.001   HIS D 320 
 PHE   0.016   0.001   PHE D 273 
 TYR   0.019   0.001   TYR C 104 
 ARG   0.014   0.000   ARG D 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14069 (  568)
  hydrogen bonds       : angle       5.44009 ( 1571)
  covalent geometry    : bond        0.00267 (16577)
  covalent geometry    : angle       0.62255 (22744)

*********************** 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  : 1.601 
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: 0.2863
  time to fit residues: 49.8379
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  : 1.587 
-------------------------------------------------------------------------------
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 152 optimal weight:    0.7980
   chunk 137 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 141 optimal weight:    6.9990
   chunk 54 optimal weight:   20.0000
   chunk 86 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 164 optimal weight:    0.8980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 295 GLN
A 296 ASN
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 ASN
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
D 405 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.093697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.071138 restraints weight = 55882.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 4.71
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  16577  Z= 0.200
  Angle     :  0.637   8.629  22744  Z= 0.331
  Chirality :  0.045   0.341   2456
  Planarity :  0.004   0.049   2595
  Dihedral  : 17.040 151.611   2904
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.67 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 28.92 %
    Favored  : 66.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.20), residues: 1731
  helix:  0.48 (0.22), residues: 571
  sheet: -0.67 (0.30), residues: 324
  loop : -2.67 (0.19), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 124 
 HIS   0.006   0.001   HIS C 207 
 PHE   0.019   0.001   PHE D 273 
 TYR   0.023   0.001   TYR D 213 
 ARG   0.011   0.000   ARG D 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05022 (  568)
  hydrogen bonds       : angle       4.77055 ( 1571)
  covalent geometry    : bond        0.00456 (16577)
  covalent geometry    : angle       0.63715 (22744)

*********************** 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
  173 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 100
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.5993 (p90)
REVERT: A  275 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7580 (mtm-85)
REVERT: A  307 ASN cc_start: 0.7907 (t0) cc_final: 0.7559 (t0)
REVERT: A  462 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8993 (tt)
REVERT: C  111 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8734 (p-80)
REVERT: C  283 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9092 (mt)
REVERT: C  369 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8875 (pt0)
REVERT: C  388 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8960 (mp)
REVERT: C  432 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7371 (t)
REVERT: D  219 TRP cc_start: 0.8081 (m100) cc_final: 0.7342 (m100)
REVERT: D  354 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7861 (mmtp)
  outliers start: 73
  outliers final: 31
  residues processed: 162
  average time/residue: 0.2690
  time to fit residues: 66.4346
Evaluate side-chains
  134 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 94
  time to evaluate  : 1.789 
-------------------------------------------------------------------------------
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  275 ARG
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  423 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  215 CYS
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 VAL
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 C residue  490 LEU
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  118 ILE
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 106 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 124 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 155 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 217 HIS
A 251 HIS
** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 357 GLN
** C  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS
** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.093886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.071306 restraints weight = 55606.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 4.74
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    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 = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  16577  Z= 0.166
  Angle     :  0.617   8.116  22744  Z= 0.320
  Chirality :  0.045   0.321   2456
  Planarity :  0.004   0.046   2595
  Dihedral  : 16.944 153.443   2897
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 28.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.20), residues: 1731
  helix:  0.44 (0.22), residues: 575
  sheet: -0.76 (0.30), residues: 322
  loop : -2.65 (0.19), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 124 
 HIS   0.013   0.001   HIS C 111 
 PHE   0.020   0.001   PHE B 255 
 TYR   0.022   0.001   TYR D 213 
 ARG   0.006   0.000   ARG D 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04590 (  568)
  hydrogen bonds       : angle       4.63450 ( 1571)
  covalent geometry    : bond        0.00379 (16577)
  covalent geometry    : angle       0.61744 (22744)

*********************** 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
  181 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 100
  time to evaluate  : 1.833 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.5627 (p90)
REVERT: A  275 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7539 (mtm-85)
REVERT: A  307 ASN cc_start: 0.8029 (t0) cc_final: 0.7632 (t0)
REVERT: A  432 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7246 (t)
REVERT: A  462 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9009 (tt)
REVERT: A  506 TYR cc_start: 0.8957 (m-80) cc_final: 0.8627 (m-80)
REVERT: B  217 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8044 (t80)
REVERT: C   37 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.5664 (p90)
REVERT: C  232 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8479 (mmm-85)
REVERT: C  283 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9081 (mt)
REVERT: C  369 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8905 (pt0)
REVERT: C  388 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8952 (mp)
REVERT: C  488 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8014 (pm20)
REVERT: C  501 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9005 (pp)
REVERT: D  219 TRP cc_start: 0.8105 (m100) cc_final: 0.7367 (m100)
REVERT: D  354 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7854 (mmtp)
  outliers start: 81
  outliers final: 43
  residues processed: 168
  average time/residue: 0.4284
  time to fit residues: 110.4747
Evaluate side-chains
  155 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 99
  time to evaluate  : 3.007 
-------------------------------------------------------------------------------
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  275 ARG
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  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  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   53 ILE
Chi-restraints excluded: chain B residue   62 ILE
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  310 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   88 SER
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  232 ARG
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  369 GLU
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  488 GLU
Chi-restraints excluded: chain C residue  490 LEU
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  418 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 140 optimal weight:    9.9990
   chunk 94 optimal weight:    4.9990
   chunk 130 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0980
   chunk 21 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
B 357 GLN
** C  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS
** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.094757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.072086 restraints weight = 55452.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 4.77
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    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 = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16577  Z= 0.135
  Angle     :  0.585   7.703  22744  Z= 0.303
  Chirality :  0.044   0.291   2456
  Planarity :  0.004   0.044   2595
  Dihedral  : 16.857 155.116   2897
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 27.96 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.20), residues: 1731
  helix:  0.65 (0.22), residues: 568
  sheet: -0.72 (0.30), residues: 324
  loop : -2.58 (0.19), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 124 
 HIS   0.006   0.001   HIS C  67 
 PHE   0.018   0.001   PHE B 255 
 TYR   0.019   0.001   TYR D 213 
 ARG   0.002   0.000   ARG C 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04002 (  568)
  hydrogen bonds       : angle       4.46478 ( 1571)
  covalent geometry    : bond        0.00303 (16577)
  covalent geometry    : angle       0.58456 (22744)

*********************** 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
  180 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 99
  time to evaluate  : 1.453 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.5954 (p90)
REVERT: A  307 ASN cc_start: 0.8388 (t0) cc_final: 0.8020 (t0)
REVERT: A  373 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8445 (m-10)
REVERT: A  506 TYR cc_start: 0.8905 (m-80) cc_final: 0.8603 (m-80)
REVERT: B  217 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8143 (t80)
REVERT: B  296 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7914 (tp30)
REVERT: B  345 MET cc_start: 0.8299 (tmm) cc_final: 0.8041 (tmm)
REVERT: C   37 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.5990 (p90)
REVERT: C  111 HIS cc_start: 0.9044 (OUTLIER) cc_final: 0.8740 (p90)
REVERT: C  369 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8883 (pt0)
REVERT: C  388 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8932 (mp)
REVERT: C  488 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7980 (pm20)
REVERT: C  501 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8981 (pp)
REVERT: D  219 TRP cc_start: 0.8087 (m100) cc_final: 0.7347 (m100)
REVERT: D  354 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7812 (mmtp)
  outliers start: 81
  outliers final: 49
  residues processed: 169
  average time/residue: 0.2680
  time to fit residues: 68.5753
Evaluate side-chains
  153 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 93
  time to evaluate  : 1.798 
-------------------------------------------------------------------------------
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  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  373 PHE
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   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  290 THR
Chi-restraints excluded: chain B residue  296 GLU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  111 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  369 GLU
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  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 82 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 175 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 172 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 153 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 145 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 357 GLN
** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.094149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.071558 restraints weight = 56507.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 4.77
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    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 = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  16577  Z= 0.156
  Angle     :  0.605   9.799  22744  Z= 0.311
  Chirality :  0.044   0.312   2456
  Planarity :  0.004   0.045   2595
  Dihedral  : 16.849 156.733   2897
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 27.57 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.20), residues: 1731
  helix:  0.65 (0.22), residues: 568
  sheet: -0.72 (0.30), residues: 318
  loop : -2.57 (0.19), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 124 
 HIS   0.013   0.001   HIS C 111 
 PHE   0.019   0.001   PHE B 255 
 TYR   0.021   0.001   TYR D 213 
 ARG   0.003   0.000   ARG D 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04227 (  568)
  hydrogen bonds       : angle       4.50959 ( 1571)
  covalent geometry    : bond        0.00355 (16577)
  covalent geometry    : angle       0.60463 (22744)

*********************** 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
  184 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 97
  time to evaluate  : 1.614 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6052 (p90)
REVERT: A  365 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7094 (p90)
REVERT: A  369 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8600 (pt0)
REVERT: A  462 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9047 (tt)
REVERT: A  506 TYR cc_start: 0.8921 (m-80) cc_final: 0.8593 (m-80)
REVERT: B   92 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5590 (pmm)
REVERT: B  217 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8202 (t80)
REVERT: B  296 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7883 (tp30)
REVERT: B  345 MET cc_start: 0.8278 (tmm) cc_final: 0.7999 (tmm)
REVERT: C   37 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.6177 (p90)
REVERT: C  111 HIS cc_start: 0.9105 (m-70) cc_final: 0.8781 (p-80)
REVERT: C  369 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8860 (pt0)
REVERT: C  388 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8940 (mp)
REVERT: C  488 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7985 (pm20)
REVERT: C  501 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8980 (pp)
REVERT: D  219 TRP cc_start: 0.8062 (m100) cc_final: 0.7312 (m100)
REVERT: D  354 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7819 (mmtp)
REVERT: D  406 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8671 (mmtm)
  outliers start: 87
  outliers final: 54
  residues processed: 171
  average time/residue: 0.2707
  time to fit residues: 72.4753
Evaluate side-chains
  160 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 92
  time to evaluate  : 1.564 
-------------------------------------------------------------------------------
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  283 LEU
Chi-restraints excluded: chain A residue  288 ILE
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   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  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   43 VAL
Chi-restraints excluded: chain C residue   88 SER
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  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   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  159 LEU
Chi-restraints excluded: chain D residue  165 ILE
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  265 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 130 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 166 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 175 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
C 111 HIS
** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.094565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.071959 restraints weight = 55914.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 4.81
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    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 = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16577  Z= 0.141
  Angle     :  0.598   8.093  22744  Z= 0.307
  Chirality :  0.044   0.301   2456
  Planarity :  0.004   0.045   2595
  Dihedral  : 16.814 157.967   2897
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 27.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.20), residues: 1731
  helix:  0.69 (0.22), residues: 568
  sheet: -0.58 (0.30), residues: 334
  loop : -2.56 (0.19), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 124 
 HIS   0.007   0.001   HIS C  67 
 PHE   0.019   0.001   PHE B 255 
 TYR   0.018   0.001   TYR D 213 
 ARG   0.002   0.000   ARG D 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  568)
  hydrogen bonds       : angle       4.44821 ( 1571)
  covalent geometry    : bond        0.00320 (16577)
  covalent geometry    : angle       0.59847 (22744)

*********************** 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
  191 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 101
  time to evaluate  : 1.755 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.6117 (p90)
REVERT: A  365 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.7094 (p90)
REVERT: A  369 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8575 (pt0)
REVERT: A  506 TYR cc_start: 0.8920 (m-80) cc_final: 0.8603 (m-80)
REVERT: B   92 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5771 (pmm)
REVERT: B  217 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8209 (t80)
REVERT: B  296 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7798 (tp30)
REVERT: C   37 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.6164 (p90)
REVERT: C  111 HIS cc_start: 0.9048 (m90) cc_final: 0.8798 (p90)
REVERT: C  283 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9151 (mp)
REVERT: C  369 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8874 (pt0)
REVERT: C  488 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7966 (pm20)
REVERT: C  501 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.8989 (pp)
REVERT: D  219 TRP cc_start: 0.8032 (m100) cc_final: 0.7297 (m100)
REVERT: D  354 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7814 (mmtp)
  outliers start: 90
  outliers final: 66
  residues processed: 178
  average time/residue: 0.2565
  time to fit residues: 71.3236
Evaluate side-chains
  169 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 91
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
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  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  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  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   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   92 MET
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  156 GLN
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  370 ASN
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   67 HIS
Chi-restraints excluded: chain C residue   88 SER
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  283 LEU
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  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   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  225 HIS
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  265 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 96 optimal weight:    0.0870
   chunk 0 optimal weight:    4.9990
   chunk 126 optimal weight:    4.9990
   chunk 159 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 108 optimal weight:   10.0000
   chunk 105 optimal weight:    2.9990
   overall best weight:    2.6166

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 138 GLN
D 340 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.091555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.068927 restraints weight = 56445.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 4.72
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  16577  Z= 0.275
  Angle     :  0.712  13.677  22744  Z= 0.367
  Chirality :  0.049   0.406   2456
  Planarity :  0.004   0.047   2595
  Dihedral  : 17.073 160.294   2897
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 27.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.20), residues: 1731
  helix:  0.47 (0.22), residues: 565
  sheet: -0.81 (0.30), residues: 333
  loop : -2.68 (0.19), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 124 
 HIS   0.010   0.001   HIS C  67 
 PHE   0.021   0.002   PHE B 255 
 TYR   0.032   0.002   TYR D 213 
 ARG   0.003   0.000   ARG B  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05649 (  568)
  hydrogen bonds       : angle       4.91260 ( 1571)
  covalent geometry    : bond        0.00631 (16577)
  covalent geometry    : angle       0.71180 (22744)

*********************** 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
  190 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 92
  time to evaluate  : 2.400 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.6926 (p90)
REVERT: A   94 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8611 (ptpp)
REVERT: A  365 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7207 (p90)
REVERT: A  432 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7626 (t)
REVERT: A  462 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9065 (tt)
REVERT: B   92 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.6057 (pmm)
REVERT: B  217 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8269 (t80)
REVERT: B  255 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7878 (p90)
REVERT: B  345 MET cc_start: 0.8619 (tmm) cc_final: 0.8213 (tmm)
REVERT: C   37 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.6696 (p90)
REVERT: C  111 HIS cc_start: 0.9120 (m90) cc_final: 0.8876 (p90)
REVERT: C  203 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7080 (t70)
REVERT: C  283 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9039 (mp)
REVERT: C  369 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8722 (pt0)
REVERT: C  488 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8040 (pm20)
REVERT: C  501 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9070 (pp)
REVERT: D  219 TRP cc_start: 0.8015 (m100) cc_final: 0.7320 (m100)
REVERT: D  354 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7937 (mmtp)
REVERT: D  406 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8685 (mmtm)
  outliers start: 98
  outliers final: 64
  residues processed: 178
  average time/residue: 0.2644
  time to fit residues: 73.2145
Evaluate side-chains
  169 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 89
  time to evaluate  : 2.775 
-------------------------------------------------------------------------------
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   94 LYS
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  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  303 MET
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  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   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  350 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   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  203 ASP
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  234 PHE
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  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
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   78 LEU
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  265 ILE
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain D residue  353 SER
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  370 ASN
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 169 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 179 optimal weight:    3.9990
   chunk 150 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 141 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 357 GLN
** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 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 = 0.3605 r_free = 0.3605 target = 0.091604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.069095 restraints weight = 56405.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 4.73
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3112 r_free = 0.3112    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  16577  Z= 0.266
  Angle     :  0.709  10.891  22744  Z= 0.366
  Chirality :  0.048   0.386   2456
  Planarity :  0.004   0.049   2595
  Dihedral  : 17.121 161.686   2897
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.53 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 28.28 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.19), residues: 1731
  helix:  0.34 (0.21), residues: 565
  sheet: -0.80 (0.30), residues: 320
  loop : -2.76 (0.19), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 124 
 HIS   0.011   0.001   HIS C  67 
 PHE   0.021   0.002   PHE B 255 
 TYR   0.032   0.002   TYR D 213 
 ARG   0.002   0.000   ARG D 250 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05469 (  568)
  hydrogen bonds       : angle       4.88875 ( 1571)
  covalent geometry    : bond        0.00611 (16577)
  covalent geometry    : angle       0.70915 (22744)

*********************** 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
  185 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 95
    poor density    : 90
  time to evaluate  : 1.605 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7051 (p90)
REVERT: A   94 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8635 (ptpp)
REVERT: A  365 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7137 (p90)
REVERT: A  432 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7647 (t)
REVERT: A  462 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9073 (tt)
REVERT: B   92 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.6054 (pmm)
REVERT: B  217 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8269 (t80)
REVERT: B  255 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7870 (p90)
REVERT: B  345 MET cc_start: 0.8593 (tmm) cc_final: 0.8164 (tmm)
REVERT: C   37 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.6738 (p90)
REVERT: C  111 HIS cc_start: 0.9080 (m90) cc_final: 0.8836 (p90)
REVERT: C  203 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7060 (t70)
REVERT: C  283 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9091 (mp)
REVERT: C  369 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8698 (pt0)
REVERT: C  488 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8043 (pm20)
REVERT: C  501 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9121 (pp)
REVERT: D  219 TRP cc_start: 0.8007 (m100) cc_final: 0.7393 (m100)
REVERT: D  354 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7948 (mmtp)
REVERT: D  406 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8687 (mmtm)
  outliers start: 95
  outliers final: 67
  residues processed: 174
  average time/residue: 0.2462
  time to fit residues: 66.6936
Evaluate side-chains
  173 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 90
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
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   94 LYS
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  271 LEU
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  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  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   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   92 MET
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  191 ASP
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  310 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain C residue   13 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   88 SER
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  203 ASP
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  234 PHE
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  369 GLU
Chi-restraints excluded: chain C residue  383 LEU
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   78 LEU
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  265 ILE
Chi-restraints excluded: chain D residue  269 ILE
Chi-restraints excluded: chain D residue  353 SER
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  370 ASN
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 163 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 149 optimal weight:    0.5980
   chunk 134 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 150 optimal weight:    2.9990
   chunk 153 optimal weight:    0.0970
   chunk 17 optimal weight:    5.9990
   chunk 177 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 122 ASN
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 GLN ** 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 = 0.3669 r_free = 0.3669 target = 0.094794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.072263 restraints weight = 55343.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 4.74
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    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 = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1833

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= 0.123
  Angle     :  0.622  13.358  22744  Z= 0.315
  Chirality :  0.045   0.270   2456
  Planarity :  0.004   0.049   2595
  Dihedral  : 16.906 162.736   2897
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 30.08 %
    Favored  : 66.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.20), residues: 1731
  helix:  0.65 (0.22), residues: 562
  sheet: -0.74 (0.31), residues: 317
  loop : -2.53 (0.19), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  20 
 HIS   0.006   0.001   HIS C  67 
 PHE   0.017   0.001   PHE B 255 
 TYR   0.014   0.001   TYR D 213 
 ARG   0.002   0.000   ARG D 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03727 (  568)
  hydrogen bonds       : angle       4.45648 ( 1571)
  covalent geometry    : bond        0.00275 (16577)
  covalent geometry    : angle       0.62214 (22744)

*********************** 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
  157 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 96
  time to evaluate  : 2.453 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.6538 (p90)
REVERT: A   94 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8498 (ptpp)
REVERT: A  303 MET cc_start: 0.7114 (mmm) cc_final: 0.6767 (mmt)
REVERT: A  506 TYR cc_start: 0.8912 (m-80) cc_final: 0.8605 (m-80)
REVERT: B   92 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5871 (pmm)
REVERT: B  217 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8075 (t80)
REVERT: B  296 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8102 (tp30)
REVERT: B  345 MET cc_start: 0.8614 (tmm) cc_final: 0.8150 (tmm)
REVERT: C   37 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.6361 (p90)
REVERT: C   56 TYR cc_start: 0.8944 (t80) cc_final: 0.8730 (t80)
REVERT: C  111 HIS cc_start: 0.9056 (m90) cc_final: 0.8833 (p90)
REVERT: C  203 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6857 (t70)
REVERT: C  369 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8738 (pt0)
REVERT: C  501 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9048 (pp)
REVERT: D  219 TRP cc_start: 0.8031 (m100) cc_final: 0.7355 (m100)
REVERT: D  354 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7818 (mmtp)
  outliers start: 61
  outliers final: 44
  residues processed: 148
  average time/residue: 0.3502
  time to fit residues: 82.6323
Evaluate side-chains
  142 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 88
  time to evaluate  : 2.505 
-------------------------------------------------------------------------------
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   94 LYS
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  317 VAL
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  490 LEU
Chi-restraints excluded: chain B residue   14 ASP
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  156 GLN
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  217 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  296 GLU
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   67 HIS
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  203 ASP
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  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
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  165 ILE
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  370 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 167 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 143 optimal weight:    3.9990
   chunk 159 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.092800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.070267 restraints weight = 56181.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 4.73
r_work (final): 0.3142
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  16577  Z= 0.198
  Angle     :  0.668  13.393  22744  Z= 0.340
  Chirality :  0.046   0.339   2456
  Planarity :  0.004   0.049   2595
  Dihedral  : 16.973 162.490   2897
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 30.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.20), residues: 1731
  helix:  0.57 (0.22), residues: 566
  sheet: -0.73 (0.30), residues: 334
  loop : -2.57 (0.20), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 124 
 HIS   0.008   0.001   HIS C  67 
 PHE   0.022   0.001   PHE B 255 
 TYR   0.024   0.001   TYR D 213 
 ARG   0.002   0.000   ARG D 250 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04627 (  568)
  hydrogen bonds       : angle       4.61072 ( 1571)
  covalent geometry    : bond        0.00454 (16577)
  covalent geometry    : angle       0.66814 (22744)

********************** 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
  149 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 87
  time to evaluate  : 1.606 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.6692 (p90)
REVERT: A   94 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8500 (ptpp)
REVERT: A  365 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6905 (p90)
REVERT: A  432 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7454 (t)
REVERT: A  462 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9064 (tt)
REVERT: A  506 TYR cc_start: 0.8981 (m-80) cc_final: 0.8683 (m-80)
REVERT: B   92 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5950 (pmm)
REVERT: B  217 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8202 (t80)
REVERT: B  345 MET cc_start: 0.8652 (tmm) cc_final: 0.8161 (tmm)
REVERT: C   37 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.6535 (p90)
REVERT: C  111 HIS cc_start: 0.9079 (m90) cc_final: 0.8848 (p90)
REVERT: C  203 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6942 (t70)
REVERT: C  369 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8634 (pt0)
REVERT: C  501 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9057 (pp)
REVERT: D  219 TRP cc_start: 0.8034 (m100) cc_final: 0.7355 (m100)
REVERT: D  354 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7851 (mmtp)
  outliers start: 62
  outliers final: 47
  residues processed: 141
  average time/residue: 0.2763
  time to fit residues: 60.2640
Evaluate side-chains
  146 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 87
  time to evaluate  : 1.632 
-------------------------------------------------------------------------------
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   94 LYS
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  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  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   45 PHE
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  208 ILE
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  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   67 HIS
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  203 ASP
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  501 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain D residue    7 ILE
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  165 ILE
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  354 LYS
Chi-restraints excluded: chain D residue  370 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   chunk 149 optimal weight:    9.9990
   chunk 150 optimal weight:    6.9990
   chunk 126 optimal weight:    3.9990
   chunk 145 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.094135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.071563 restraints weight = 55820.712|
|-----------------------------------------------------------------------------|
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1923

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= 0.139
  Angle     :  0.636  13.134  22744  Z= 0.322
  Chirality :  0.045   0.297   2456
  Planarity :  0.004   0.047   2595
  Dihedral  : 16.916 162.908   2897
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.20), residues: 1731
  helix:  0.63 (0.22), residues: 564
  sheet: -0.66 (0.31), residues: 316
  loop : -2.51 (0.19), residues: 851

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 124 
 HIS   0.007   0.001   HIS C  67 
 PHE   0.020   0.001   PHE B 255 
 TYR   0.018   0.001   TYR D 213 
 ARG   0.002   0.000   ARG C 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  568)
  hydrogen bonds       : angle       4.45504 ( 1571)
  covalent geometry    : bond        0.00316 (16577)
  covalent geometry    : angle       0.63627 (22744)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8087.62 seconds
wall clock time: 147 minutes 14.66 seconds (8834.66 seconds total)