Starting phenix.real_space_refine
on Wed Feb  4 09:00:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i04_52550/02_2026/9i04_52550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i04_52550/02_2026/9i04_52550.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i04_52550/02_2026/9i04_52550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i04_52550/02_2026/9i04_52550.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i04_52550/02_2026/9i04_52550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i04_52550/02_2026/9i04_52550.map"
  }
  resolution = 4.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.027
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: 5
    Type Number    sf(0)   Gaussians
     P      28      5.49       5
     S      45      5.16       5
     C    5936      2.51       5
     N    1620      2.21       5
     O    1840      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9469
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3957
          Classifications: {'peptide': 493}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 25, 'TRANS': 467}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 4232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4232
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 25, 'TRANS': 506}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 703
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 85}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 292
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "E"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 285
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
  Time building chain proxies: 1.74, per 1000 atoms: 0.18
  Number of scatterers: 9469
  At special positions: 0
  Unit cell: (84.5973, 115.674, 132.939, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      45     16.00
     P      28     15.00
     O    1840      8.00
     N    1620      7.00
     C    5936      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: 0.77
  Conformation dependent library (CDL) restraints added in 458.5 milliseconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 10 sheets defined
      37.8% alpha, 19.6% beta
      0 base pairs and 20 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 50
    Processing helix  chain 'A' and resid 58 through 78
    Processing helix  chain 'A' and resid 112 through 121
    Processing helix  chain 'A' and resid 124 through 132
    Processing helix  chain 'A' and resid 142 through 156
    Processing helix  chain 'A' and resid 179 through 196
      removed outlier: 3.697A  pdb=" N   ALA A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 251
    Processing helix  chain 'A' and resid 330 through 339
    Processing helix  chain 'A' and resid 354 through 356
      No H-bonds generated for 'chain 'A' and resid 354 through 356'
    Processing helix  chain 'A' and resid 377 through 393
      removed outlier: 3.851A  pdb=" N   LEU A 381 " --> pdb=" O   GLY A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 470
    Processing helix  chain 'A' and resid 480 through 495
    Processing helix  chain 'A' and resid 510 through 519
    Processing helix  chain 'A' and resid 519 through 527
      removed outlier: 4.351A  pdb=" N   ASP A 523 " --> pdb=" O   GLY A 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 22
      removed outlier: 3.680A  pdb=" N   SER B  21 " --> pdb=" O   GLY B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 48
    Processing helix  chain 'B' and resid 87 through 96
      removed outlier: 3.620A  pdb=" N   LEU B  91 " --> pdb=" O   ASP B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 122
      removed outlier: 3.582A  pdb=" N   THR B 122 " --> pdb=" O   ILE B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'B' and resid 198 through 217
    Processing helix  chain 'B' and resid 218 through 222
    Processing helix  chain 'B' and resid 227 through 231
    Processing helix  chain 'B' and resid 232 through 233
      No H-bonds generated for 'chain 'B' and resid 232 through 233'
    Processing helix  chain 'B' and resid 234 through 238
    Processing helix  chain 'B' and resid 324 through 332
    Processing helix  chain 'B' and resid 352 through 356
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 437 through 441
    Processing helix  chain 'B' and resid 447 through 461
    Processing helix  chain 'B' and resid 478 through 482
      removed outlier: 3.645A  pdb=" N   LYS B 481 " --> pdb=" O   PRO B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 500
      removed outlier: 3.871A  pdb=" N   GLN B 488 " --> pdb=" O   ASN B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 517
      removed outlier: 3.606A  pdb=" N   TRP B 513 " --> pdb=" O   GLN B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 535
      removed outlier: 3.699A  pdb=" N   THR B 523 " --> pdb=" O   PRO B 519 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   ILE B 528 " --> pdb=" O   THR B 524 " (cutoff:3.500A)
      Proline residue:  B 529  - end of helix
      removed outlier: 3.579A  pdb=" N   THR B 535 " --> pdb=" O   SER B 531 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 53
    Processing helix  chain 'C' and resid 75 through 89
    Processing helix  chain 'C' and resid 101 through 112
      removed outlier: 3.652A  pdb=" N   LEU C 105 " --> pdb=" O   ASP C 101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109
      removed outlier: 5.071A  pdb=" N   VAL A 104 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   PHE A  87 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU A 108 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   LEU A  83 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   LEU A  38 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
      removed outlier: 8.193A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   PHE A  40 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   TYR A  88 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL A  42 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASP A  43 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   ILE A 166 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   MET A 203 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LEU A 168 " --> pdb=" O   MET A 203 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262
      removed outlier: 3.666A  pdb=" N   SER A 257 " --> pdb=" O   ILE A 273 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   VAL A 394 " --> pdb=" O   PRO A 415 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ALA A 395 " --> pdb=" O   PHE A 350 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   PHE A 350 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A 397 " --> pdb=" O   MET A 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 304
    Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 329
    Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 84
      removed outlier: 5.373A  pdb=" N   VAL B  79 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LEU B  58 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LEU B  83 " --> pdb=" O   ILE B  54 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   ILE B  54 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG B 130 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   GLN B 162 " --> pdb=" O   ARG B 130 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   ILE B 132 " --> pdb=" O   GLN B 162 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   PHE B 164 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ILE B 134 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
      removed outlier: 9.087A  pdb=" N   TYR B 225 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   PHE B 163 " --> pdb=" O   TYR B 225 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 247 through 253
      removed outlier: 6.804A  pdb=" N   VAL B 361 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   LEU B 268 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 9.561A  pdb=" N   ASN B 359 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   GLN B 360 " --> pdb=" O   GLN B 423 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   GLN B 423 " --> pdb=" O   GLN B 360 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ALA B 366 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 10.266A  pdb=" N   GLU B 417 " --> pdb=" O   ALA B 366 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   VAL B 405 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      removed outlier: 8.862A  pdb=" N   MET B 389 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL B 390 " --> pdb=" O   PHE B 345 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   PHE B 345 " --> pdb=" O   VAL B 390 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ILE B 392 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   PHE B 340 " --> pdb=" O   PRO B 248 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   ARG B 250 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   VAL B 342 " --> pdb=" O   ARG B 250 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   THR B 252 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   GLY B 344 " --> pdb=" O   THR B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 316
    Processing sheet with id=AA9, first strand: chain 'B' and resid 464 through 467
    Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 59
      removed outlier: 6.094A  pdb=" N   ILE C  32 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL C  70 " --> pdb=" O   TYR C  33 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1086 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      20 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2604
        1.33 -     1.45: 1612
        1.45 -     1.57: 5370
        1.57 -     1.69: 54
        1.69 -     1.81: 74
  Bond restraints: 9714
  Sorted by residual:
  bond pdb=" C3'  DT E  10 "
       pdb=" O3'  DT E  10 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.19e+00
  bond pdb=" C3'  DG E   8 "
       pdb=" O3'  DG E   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.454 -0.032 3.00e-02 1.11e+03 1.12e+00
  bond pdb=" C3'  DT E   7 "
       pdb=" C2'  DT E   7 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 8.97e-01
  bond pdb=" CA  ASP A  81 "
       pdb=" C   ASP A  81 "
    ideal  model  delta    sigma   weight residual
    1.532  1.523  0.009 9.60e-03 1.09e+04 8.88e-01
  bond pdb=" CA  VAL A 504 "
       pdb=" CB  VAL A 504 "
    ideal  model  delta    sigma   weight residual
    1.540  1.528  0.012 1.36e-02 5.41e+03 8.43e-01
  ... (remaining 9709 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 12912
        1.51 -     3.02: 267
        3.02 -     4.53: 42
        4.53 -     6.04: 10
        6.04 -     7.55: 2
  Bond angle restraints: 13233
  Sorted by residual:
  angle pdb=" C   GLN B 330 "
        pdb=" N   MET B 331 "
        pdb=" CA  MET B 331 "
      ideal   model   delta    sigma   weight residual
     122.60  117.41    5.19 1.56e+00 4.11e-01 1.11e+01
  angle pdb=" C   THR A 334 "
        pdb=" N   GLU A 335 "
        pdb=" CA  GLU A 335 "
      ideal   model   delta    sigma   weight residual
     120.72  115.27    5.45 1.67e+00 3.59e-01 1.07e+01
  angle pdb=" C   LYS A 526 "
        pdb=" N   GLU A 527 "
        pdb=" CA  GLU A 527 "
      ideal   model   delta    sigma   weight residual
     121.18  115.63    5.55 1.98e+00 2.55e-01 7.87e+00
  angle pdb=" N   GLU A 527 "
        pdb=" CA  GLU A 527 "
        pdb=" CB  GLU A 527 "
      ideal   model   delta    sigma   weight residual
     110.39  115.29   -4.90 1.75e+00 3.27e-01 7.84e+00
  angle pdb=" C   GLN B 527 "
        pdb=" N   ILE B 528 "
        pdb=" CA  ILE B 528 "
      ideal   model   delta    sigma   weight residual
     120.33  122.27   -1.94 8.00e-01 1.56e+00 5.90e+00
  ... (remaining 13228 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.13: 5556
       30.13 -    60.27: 297
       60.27 -    90.40: 32
       90.40 -   120.53: 1
      120.53 -   150.66: 1
  Dihedral angle restraints: 5887
    sinusoidal: 2620
      harmonic: 3267
  Sorted by residual:
  dihedral pdb=" C4'  DT E  10 "
           pdb=" C3'  DT E  10 "
           pdb=" O3'  DT E  10 "
           pdb=" P    DG E  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   10.66 -150.66     1      3.50e+01 8.16e-04 1.47e+01
  dihedral pdb=" CA  ASP B 177 "
           pdb=" CB  ASP B 177 "
           pdb=" CG  ASP B 177 "
           pdb=" OD1 ASP B 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.40   57.40     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  SER B 318 "
           pdb=" C   SER B 318 "
           pdb=" N   ASP B 319 "
           pdb=" CA  ASP B 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 5884 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 974
       0.033 -    0.065: 350
       0.065 -    0.098: 102
       0.098 -    0.130: 54
       0.130 -    0.163: 3
  Chirality restraints: 1483
  Sorted by residual:
  chirality pdb=" CA  GLU C  36 "
            pdb=" N   GLU C  36 "
            pdb=" C   GLU C  36 "
            pdb=" CB  GLU C  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.64e-01
  chirality pdb=" CG  LEU A 147 "
            pdb=" CB  LEU A 147 "
            pdb=" CD1 LEU A 147 "
            pdb=" CD2 LEU A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.41e-01
  chirality pdb=" P    DG E  11 "
            pdb=" OP1  DG E  11 "
            pdb=" OP2  DG E  11 "
            pdb=" O5'  DG E  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 1480 not shown)

  Planarity restraints: 1615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT E   7 "   -0.022 2.00e-02 2.50e+03   1.05e-02 2.77e+00
        pdb=" N1   DT E   7 "    0.022 2.00e-02 2.50e+03
        pdb=" C2   DT E   7 "    0.003 2.00e-02 2.50e+03
        pdb=" O2   DT E   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DT E   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DT E   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4   DT E   7 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DT E   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT E   7 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DT E   7 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 115 "    0.025 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO C 116 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C 116 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 116 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 216 "   -0.008 2.00e-02 2.50e+03   1.53e-02 2.34e+00
        pdb=" C   GLU B 216 "    0.026 2.00e-02 2.50e+03
        pdb=" O   GLU B 216 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLY B 217 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1612 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 4235
        2.94 -     3.43: 10666
        3.43 -     3.92: 16981
        3.92 -     4.41: 19190
        4.41 -     4.90: 28855
  Nonbonded interactions: 79927
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 523 "
            pdb=" OE1 GLU A 527 "
     model   vdw
     2.451 3.040
  nonbonded pdb=" O   LYS A 331 "
            pdb=" OE1 GLU A 335 "
     model   vdw
     2.531 3.040
  nonbonded pdb=" O5'  DG E   6 "
            pdb=" O4'  DG E   6 "
     model   vdw
     2.533 2.432
  nonbonded pdb=" O   LYS A 331 "
            pdb=" OG1 THR A 334 "
     model   vdw
     2.564 3.040
  nonbonded pdb=" N1   DG E  11 "
            pdb=" C4   DG E  11 "
     model   vdw
     2.595 2.672
  ... (remaining 79922 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.320
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
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   0.033   9714  Z= 0.122
  Angle     :  0.548   7.548  13233  Z= 0.296
  Chirality :  0.041   0.163   1483
  Planarity :  0.004   0.042   1615
  Dihedral  : 17.414 150.663   3761
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.26), residues: 1112
  helix:  1.25 (0.26), residues: 386
  sheet: -0.97 (0.36), residues: 185
  loop : -0.10 (0.29), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 325 
 TYR   0.007   0.001   TYR B 333 
 PHE   0.009   0.001   PHE B 323 
 TRP   0.007   0.001   TRP C  82 
 HIS   0.002   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9714)
  covalent geometry    : angle       0.54840 (13233)
  hydrogen bonds       : bond        0.11601 (  390)
  hydrogen bonds       : angle       6.31110 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9480 (mpp) cc_final: 0.9265 (mpp)
REVERT: A  135 MET cc_start: 0.8522 (mpp) cc_final: 0.8320 (mpp)
REVERT: A  167 MET cc_start: 0.9107 (tpp) cc_final: 0.8488 (tpp)
REVERT: A  168 LEU cc_start: 0.9851 (tp) cc_final: 0.9124 (tp)
REVERT: A  203 MET cc_start: 0.8907 (mpp) cc_final: 0.7437 (mpp)
REVERT: A  279 LYS cc_start: 0.9411 (mmtt) cc_final: 0.8495 (mmtt)
REVERT: A  346 MET cc_start: 0.8683 (tpt) cc_final: 0.8384 (tpp)
REVERT: A  348 MET cc_start: 0.9467 (mmp) cc_final: 0.8547 (mmm)
REVERT: A  514 MET cc_start: 0.9090 (ptt) cc_final: 0.8550 (ptt)
REVERT: B   20 MET cc_start: 0.7293 (mmp) cc_final: 0.7039 (mmm)
REVERT: B   84 MET cc_start: 0.9498 (pmm) cc_final: 0.9164 (pmm)
REVERT: B  212 MET cc_start: 0.9643 (mmp) cc_final: 0.9425 (mmm)
REVERT: B  389 MET cc_start: 0.8098 (tpp) cc_final: 0.7450 (tpp)
REVERT: B  461 MET cc_start: 0.9086 (ttt) cc_final: 0.8425 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0954
  time to fit residues: 9.1877
Evaluate side-chains
  51 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.0670
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    6.9990
   overall best weight:    2.4122

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 320 GLN
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.037223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.028377 restraints weight = 86922.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.029317 restraints weight = 52301.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.029956 restraints weight = 37515.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.030397 restraints weight = 29982.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.030680 restraints weight = 25772.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.0685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9714  Z= 0.179
  Angle     :  0.546   7.652  13233  Z= 0.291
  Chirality :  0.040   0.150   1483
  Planarity :  0.004   0.037   1615
  Dihedral  : 17.316 152.935   1495
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.94 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.26), residues: 1112
  helix:  1.30 (0.26), residues: 395
  sheet: -1.03 (0.36), residues: 180
  loop : -0.06 (0.30), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.010   0.001   TYR B 333 
 PHE   0.008   0.001   PHE A 131 
 TRP   0.005   0.001   TRP C 104 
 HIS   0.003   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9714)
  covalent geometry    : angle       0.54578 (13233)
  hydrogen bonds       : bond        0.03425 (  390)
  hydrogen bonds       : angle       5.39825 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9380 (mpp) cc_final: 0.9132 (mpp)
REVERT: A   87 PHE cc_start: 0.9471 (m-10) cc_final: 0.8864 (m-80)
REVERT: A  168 LEU cc_start: 0.9843 (tp) cc_final: 0.9584 (tp)
REVERT: A  203 MET cc_start: 0.8686 (mpp) cc_final: 0.8303 (mpp)
REVERT: A  279 LYS cc_start: 0.9386 (mmtt) cc_final: 0.8558 (mmtt)
REVERT: A  346 MET cc_start: 0.8779 (tpt) cc_final: 0.8564 (tpp)
REVERT: A  348 MET cc_start: 0.9435 (mmp) cc_final: 0.8579 (mmm)
REVERT: A  496 ASP cc_start: 0.9225 (t0) cc_final: 0.9020 (t0)
REVERT: B  212 MET cc_start: 0.9629 (mmp) cc_final: 0.9423 (mmm)
REVERT: B  389 MET cc_start: 0.8435 (tpp) cc_final: 0.8209 (tpp)
REVERT: B  461 MET cc_start: 0.8931 (ttt) cc_final: 0.8307 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0912
  time to fit residues: 8.3472
Evaluate side-chains
  49 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0270
   chunk 96 optimal weight:    0.0270
   chunk 76 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 103 optimal weight:    0.8980
   chunk 12 optimal weight:   10.0000
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 ASN
** B 492 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 = 0.3065 r_free = 0.3065 target = 0.038498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.029471 restraints weight = 83079.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.030444 restraints weight = 50058.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.031107 restraints weight = 35838.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.031590 restraints weight = 28568.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.031908 restraints weight = 24348.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.0760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9714  Z= 0.102
  Angle     :  0.506   6.584  13233  Z= 0.267
  Chirality :  0.041   0.152   1483
  Planarity :  0.003   0.035   1615
  Dihedral  : 17.287 151.219   1495
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.26), residues: 1112
  helix:  1.65 (0.27), residues: 383
  sheet: -0.88 (0.36), residues: 179
  loop :  0.06 (0.29), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.008   0.001   TYR B 397 
 PHE   0.008   0.001   PHE B  59 
 TRP   0.004   0.001   TRP C  82 
 HIS   0.002   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 9714)
  covalent geometry    : angle       0.50603 (13233)
  hydrogen bonds       : bond        0.03081 (  390)
  hydrogen bonds       : angle       5.04710 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.9204 (t70) cc_final: 0.8795 (t70)
REVERT: A   62 MET cc_start: 0.9335 (mpp) cc_final: 0.9005 (mmm)
REVERT: A   87 PHE cc_start: 0.9428 (m-10) cc_final: 0.8909 (m-80)
REVERT: A  135 MET cc_start: 0.8995 (mpp) cc_final: 0.8784 (mpp)
REVERT: A  168 LEU cc_start: 0.9833 (tp) cc_final: 0.9582 (tp)
REVERT: A  203 MET cc_start: 0.8674 (mpp) cc_final: 0.8340 (mpp)
REVERT: A  279 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8316 (mmtt)
REVERT: A  348 MET cc_start: 0.9360 (mmp) cc_final: 0.8604 (mmm)
REVERT: A  434 LEU cc_start: 0.9397 (tp) cc_final: 0.9188 (tp)
REVERT: A  496 ASP cc_start: 0.9198 (t0) cc_final: 0.8977 (t0)
REVERT: B  389 MET cc_start: 0.8409 (tpp) cc_final: 0.8118 (tpp)
REVERT: B  461 MET cc_start: 0.8951 (ttt) cc_final: 0.8186 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0854
  time to fit residues: 8.7299
Evaluate side-chains
  53 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0970
   chunk 29 optimal weight:    5.9990
   chunk 99 optimal weight:    0.0570
   chunk 68 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 87 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.4302

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.038250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.029322 restraints weight = 83746.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.030293 restraints weight = 50714.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.030956 restraints weight = 36290.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.031413 restraints weight = 28838.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.031719 restraints weight = 24580.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.0940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9714  Z= 0.126
  Angle     :  0.507   6.580  13233  Z= 0.268
  Chirality :  0.040   0.144   1483
  Planarity :  0.003   0.035   1615
  Dihedral  : 17.265 151.124   1495
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.27), residues: 1112
  helix:  1.81 (0.27), residues: 383
  sheet: -0.79 (0.36), residues: 184
  loop : -0.02 (0.30), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  43 
 TYR   0.010   0.001   TYR B 333 
 PHE   0.007   0.001   PHE B  59 
 TRP   0.005   0.001   TRP C  82 
 HIS   0.002   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9714)
  covalent geometry    : angle       0.50733 (13233)
  hydrogen bonds       : bond        0.02975 (  390)
  hydrogen bonds       : angle       4.97233 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.9268 (t70) cc_final: 0.8837 (t70)
REVERT: A   62 MET cc_start: 0.9341 (mpp) cc_final: 0.9111 (mmm)
REVERT: A   87 PHE cc_start: 0.9454 (m-10) cc_final: 0.8849 (m-80)
REVERT: A  168 LEU cc_start: 0.9843 (tp) cc_final: 0.9593 (tp)
REVERT: A  203 MET cc_start: 0.8687 (mpp) cc_final: 0.8339 (mpp)
REVERT: A  279 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8349 (mmtt)
REVERT: A  348 MET cc_start: 0.9130 (mmp) cc_final: 0.8534 (mmm)
REVERT: A  496 ASP cc_start: 0.9222 (t0) cc_final: 0.8992 (t0)
REVERT: A  514 MET cc_start: 0.9117 (ptt) cc_final: 0.8610 (ptt)
REVERT: B   84 MET cc_start: 0.9481 (pmm) cc_final: 0.9094 (pmm)
REVERT: B  212 MET cc_start: 0.9570 (mmp) cc_final: 0.9305 (mmm)
REVERT: B  389 MET cc_start: 0.8340 (tpp) cc_final: 0.7675 (mmm)
REVERT: B  461 MET cc_start: 0.8833 (ttt) cc_final: 0.8126 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0868
  time to fit residues: 8.7914
Evaluate side-chains
  54 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 108 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0770
   chunk 70 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   overall best weight:    1.6142

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN
** B 492 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 = 0.3054 r_free = 0.3054 target = 0.038164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.029239 restraints weight = 83856.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.030201 restraints weight = 50329.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.030867 restraints weight = 35910.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.031256 restraints weight = 28422.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.031626 restraints weight = 24520.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9714  Z= 0.131
  Angle     :  0.500   6.478  13233  Z= 0.266
  Chirality :  0.040   0.143   1483
  Planarity :  0.003   0.034   1615
  Dihedral  : 17.291 151.882   1495
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.26), residues: 1112
  helix:  1.78 (0.27), residues: 383
  sheet: -0.82 (0.36), residues: 184
  loop : -0.01 (0.30), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 400 
 TYR   0.010   0.001   TYR B 333 
 PHE   0.007   0.001   PHE B 409 
 TRP   0.005   0.001   TRP C  82 
 HIS   0.002   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9714)
  covalent geometry    : angle       0.50007 (13233)
  hydrogen bonds       : bond        0.02943 (  390)
  hydrogen bonds       : angle       4.94592 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.9286 (t70) cc_final: 0.9023 (t70)
REVERT: A   62 MET cc_start: 0.9344 (mpp) cc_final: 0.9102 (mpp)
REVERT: A   87 PHE cc_start: 0.9437 (m-10) cc_final: 0.8817 (m-80)
REVERT: A  135 MET cc_start: 0.9258 (mpp) cc_final: 0.8889 (mpp)
REVERT: A  168 LEU cc_start: 0.9853 (tp) cc_final: 0.9638 (tp)
REVERT: A  279 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8409 (mmtt)
REVERT: A  348 MET cc_start: 0.9194 (mmp) cc_final: 0.8527 (mmm)
REVERT: A  434 LEU cc_start: 0.9357 (tp) cc_final: 0.9153 (tp)
REVERT: A  496 ASP cc_start: 0.9222 (t0) cc_final: 0.8990 (t0)
REVERT: A  514 MET cc_start: 0.9135 (ptt) cc_final: 0.8713 (ptt)
REVERT: B   14 MET cc_start: 0.9354 (tpt) cc_final: 0.9003 (mmm)
REVERT: B  212 MET cc_start: 0.9510 (mmp) cc_final: 0.9285 (mmm)
REVERT: B  389 MET cc_start: 0.8615 (tpp) cc_final: 0.8033 (mmm)
REVERT: B  461 MET cc_start: 0.8876 (ttt) cc_final: 0.8149 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0954
  time to fit residues: 9.6046
Evaluate side-chains
  54 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 51 optimal weight:    0.0270
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0670
   chunk 86 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 81 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 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 = 0.3080 r_free = 0.3080 target = 0.038909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.029917 restraints weight = 81865.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.030898 restraints weight = 48970.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.031586 restraints weight = 34816.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.032063 restraints weight = 27520.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.032380 restraints weight = 23374.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9714  Z= 0.098
  Angle     :  0.498   7.335  13233  Z= 0.261
  Chirality :  0.041   0.166   1483
  Planarity :  0.003   0.037   1615
  Dihedral  : 17.284 150.145   1495
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.27), residues: 1112
  helix:  1.86 (0.27), residues: 384
  sheet: -0.66 (0.36), residues: 182
  loop :  0.08 (0.30), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 404 
 TYR   0.008   0.001   TYR A 400 
 PHE   0.008   0.001   PHE B  59 
 TRP   0.005   0.001   TRP C  82 
 HIS   0.002   0.001   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 9714)
  covalent geometry    : angle       0.49823 (13233)
  hydrogen bonds       : bond        0.02788 (  390)
  hydrogen bonds       : angle       4.75997 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.9254 (t70) cc_final: 0.8993 (t70)
REVERT: A   87 PHE cc_start: 0.9394 (m-10) cc_final: 0.8778 (m-80)
REVERT: A  135 MET cc_start: 0.9230 (mpp) cc_final: 0.8902 (mpp)
REVERT: A  167 MET cc_start: 0.9161 (tpp) cc_final: 0.8558 (mmm)
REVERT: A  168 LEU cc_start: 0.9827 (tp) cc_final: 0.9593 (tp)
REVERT: A  203 MET cc_start: 0.8326 (mpp) cc_final: 0.7719 (mpp)
REVERT: A  279 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8300 (mmtt)
REVERT: A  348 MET cc_start: 0.9013 (mmp) cc_final: 0.8502 (mmm)
REVERT: A  434 LEU cc_start: 0.9284 (tp) cc_final: 0.9059 (tp)
REVERT: A  496 ASP cc_start: 0.9182 (t0) cc_final: 0.8933 (t0)
REVERT: A  514 MET cc_start: 0.9161 (ptt) cc_final: 0.8495 (ppp)
REVERT: B   14 MET cc_start: 0.9233 (tpt) cc_final: 0.8904 (mmm)
REVERT: B   40 MET cc_start: 0.9341 (tmm) cc_final: 0.9120 (tmm)
REVERT: B   84 MET cc_start: 0.9418 (pmm) cc_final: 0.9011 (pmm)
REVERT: B  389 MET cc_start: 0.8527 (tpp) cc_final: 0.7991 (mmm)
REVERT: B  461 MET cc_start: 0.8748 (ttt) cc_final: 0.8003 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0904
  time to fit residues: 8.8242
Evaluate side-chains
  53 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 112 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   chunk 104 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 101 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 84 optimal weight:    7.9990
   overall best weight:    1.0762

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN
** B 492 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 = 0.3068 r_free = 0.3068 target = 0.038647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.029751 restraints weight = 82610.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.030713 restraints weight = 49607.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.031390 restraints weight = 35401.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.031841 restraints weight = 27978.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.032178 restraints weight = 23816.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9714  Z= 0.109
  Angle     :  0.502   7.239  13233  Z= 0.263
  Chirality :  0.040   0.156   1483
  Planarity :  0.003   0.039   1615
  Dihedral  : 17.253 149.900   1495
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.27), residues: 1112
  helix:  1.88 (0.27), residues: 384
  sheet: -0.68 (0.36), residues: 184
  loop :  0.11 (0.30), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 403 
 TYR   0.008   0.001   TYR A 400 
 PHE   0.007   0.001   PHE B  59 
 TRP   0.005   0.001   TRP C  82 
 HIS   0.002   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9714)
  covalent geometry    : angle       0.50180 (13233)
  hydrogen bonds       : bond        0.02787 (  390)
  hydrogen bonds       : angle       4.77268 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.9261 (t70) cc_final: 0.8805 (t70)
REVERT: A   62 MET cc_start: 0.9355 (mpp) cc_final: 0.9130 (mpp)
REVERT: A   87 PHE cc_start: 0.9419 (m-10) cc_final: 0.8798 (m-80)
REVERT: A  135 MET cc_start: 0.9245 (mpp) cc_final: 0.8904 (mpp)
REVERT: A  167 MET cc_start: 0.9176 (tpp) cc_final: 0.8569 (mmm)
REVERT: A  168 LEU cc_start: 0.9830 (tp) cc_final: 0.9605 (tp)
REVERT: A  279 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8311 (mmtt)
REVERT: A  348 MET cc_start: 0.9064 (mmp) cc_final: 0.8487 (mmm)
REVERT: A  434 LEU cc_start: 0.9315 (tp) cc_final: 0.9090 (tp)
REVERT: A  496 ASP cc_start: 0.9196 (t0) cc_final: 0.8947 (t0)
REVERT: B  212 MET cc_start: 0.9595 (mmp) cc_final: 0.9348 (mmm)
REVERT: B  389 MET cc_start: 0.8541 (tpp) cc_final: 0.7991 (mmm)
REVERT: B  461 MET cc_start: 0.8836 (ttt) cc_final: 0.8083 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0722
  time to fit residues: 6.9497
Evaluate side-chains
  56 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 56 optimal weight:    0.2980
   chunk 90 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0870
   chunk 40 optimal weight:    0.7980
   chunk 106 optimal weight:    8.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN
** B 492 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 = 0.3084 r_free = 0.3084 target = 0.039138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.030135 restraints weight = 83200.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.031119 restraints weight = 49966.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.031800 restraints weight = 35667.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.032278 restraints weight = 28321.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.032601 restraints weight = 24077.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   9714  Z= 0.099
  Angle     :  0.505   7.518  13233  Z= 0.263
  Chirality :  0.041   0.161   1483
  Planarity :  0.003   0.040   1615
  Dihedral  : 17.245 149.107   1495
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.27), residues: 1112
  helix:  1.87 (0.27), residues: 384
  sheet: -0.56 (0.36), residues: 182
  loop :  0.11 (0.30), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 403 
 TYR   0.008   0.001   TYR A 400 
 PHE   0.014   0.001   PHE B 135 
 TRP   0.005   0.001   TRP C  82 
 HIS   0.002   0.000   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 9714)
  covalent geometry    : angle       0.50484 (13233)
  hydrogen bonds       : bond        0.02734 (  390)
  hydrogen bonds       : angle       4.69279 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.9268 (t70) cc_final: 0.8991 (t70)
REVERT: A   62 MET cc_start: 0.9325 (mpp) cc_final: 0.9090 (mpp)
REVERT: A   87 PHE cc_start: 0.9431 (m-10) cc_final: 0.8895 (m-80)
REVERT: A  135 MET cc_start: 0.9252 (mpp) cc_final: 0.9022 (mmt)
REVERT: A  167 MET cc_start: 0.9174 (tpp) cc_final: 0.8560 (mmm)
REVERT: A  168 LEU cc_start: 0.9826 (tp) cc_final: 0.9604 (tp)
REVERT: A  203 MET cc_start: 0.8202 (mpp) cc_final: 0.7608 (mpp)
REVERT: A  279 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8301 (mmtt)
REVERT: A  348 MET cc_start: 0.9047 (mmp) cc_final: 0.8480 (mmm)
REVERT: A  434 LEU cc_start: 0.9302 (tp) cc_final: 0.9073 (tp)
REVERT: A  496 ASP cc_start: 0.9185 (t0) cc_final: 0.8933 (t0)
REVERT: A  514 MET cc_start: 0.9113 (ptt) cc_final: 0.8521 (ppp)
REVERT: B   14 MET cc_start: 0.8015 (mmp) cc_final: 0.7308 (mmm)
REVERT: B   84 MET cc_start: 0.9411 (pmm) cc_final: 0.9078 (pmm)
REVERT: B  212 MET cc_start: 0.9625 (mmp) cc_final: 0.9410 (mmm)
REVERT: B  389 MET cc_start: 0.8528 (tpp) cc_final: 0.8033 (mmm)
REVERT: B  461 MET cc_start: 0.8816 (ttt) cc_final: 0.8056 (ttt)
REVERT: B  495 LEU cc_start: 0.9723 (tt) cc_final: 0.9400 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0782
  time to fit residues: 7.6031
Evaluate side-chains
  54 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9990
   chunk 108 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9980
   chunk 101 optimal weight:    0.0970
   chunk 64 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  65 GLN
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN
** B 492 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 = 0.3083 r_free = 0.3083 target = 0.039047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.030072 restraints weight = 82425.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.031047 restraints weight = 50012.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.031737 restraints weight = 35858.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.032186 restraints weight = 28386.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.032532 restraints weight = 24200.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.062   9714  Z= 0.103
  Angle     :  0.492   7.405  13233  Z= 0.257
  Chirality :  0.040   0.158   1483
  Planarity :  0.003   0.039   1615
  Dihedral  : 17.219 148.726   1495
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.27), residues: 1112
  helix:  1.95 (0.27), residues: 383
  sheet: -0.53 (0.36), residues: 182
  loop :  0.16 (0.30), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.008   0.001   TYR A 400 
 PHE   0.006   0.001   PHE B  31 
 TRP   0.006   0.001   TRP C  82 
 HIS   0.002   0.000   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 9714)
  covalent geometry    : angle       0.49154 (13233)
  hydrogen bonds       : bond        0.02677 (  390)
  hydrogen bonds       : angle       4.65697 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.9236 (t70) cc_final: 0.8981 (t70)
REVERT: A   62 MET cc_start: 0.9325 (mpp) cc_final: 0.9096 (mpp)
REVERT: A   87 PHE cc_start: 0.9438 (m-10) cc_final: 0.9027 (m-80)
REVERT: A  135 MET cc_start: 0.9261 (mpp) cc_final: 0.9012 (mmt)
REVERT: A  167 MET cc_start: 0.9188 (tpp) cc_final: 0.8566 (mmm)
REVERT: A  279 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8278 (mmtt)
REVERT: A  348 MET cc_start: 0.9090 (mmp) cc_final: 0.8485 (mmm)
REVERT: A  434 LEU cc_start: 0.9327 (tp) cc_final: 0.9096 (tp)
REVERT: A  496 ASP cc_start: 0.9241 (t0) cc_final: 0.8986 (t0)
REVERT: A  514 MET cc_start: 0.9161 (ptt) cc_final: 0.8606 (ppp)
REVERT: B   14 MET cc_start: 0.7985 (mmp) cc_final: 0.7273 (mmm)
REVERT: B   84 MET cc_start: 0.9168 (pmm) cc_final: 0.8857 (pmm)
REVERT: B  212 MET cc_start: 0.9619 (mmp) cc_final: 0.9410 (mmm)
REVERT: B  389 MET cc_start: 0.8540 (tpp) cc_final: 0.8037 (mmm)
REVERT: B  461 MET cc_start: 0.8843 (ttt) cc_final: 0.8085 (ttt)
REVERT: B  495 LEU cc_start: 0.9719 (tt) cc_final: 0.9395 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0682
  time to fit residues: 7.0193
Evaluate side-chains
  56 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 104 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9980
   chunk 92 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.038066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.029176 restraints weight = 83450.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.030118 restraints weight = 50607.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.030778 restraints weight = 36415.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.031233 restraints weight = 29044.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.031536 restraints weight = 24779.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9714  Z= 0.146
  Angle     :  0.515   6.908  13233  Z= 0.270
  Chirality :  0.040   0.156   1483
  Planarity :  0.003   0.040   1615
  Dihedral  : 17.251 151.051   1495
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.27), residues: 1112
  helix:  1.95 (0.27), residues: 383
  sheet: -0.73 (0.36), residues: 184
  loop :  0.18 (0.30), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 400 
 TYR   0.009   0.001   TYR B 333 
 PHE   0.009   0.001   PHE B 409 
 TRP   0.007   0.001   TRP C  82 
 HIS   0.003   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9714)
  covalent geometry    : angle       0.51456 (13233)
  hydrogen bonds       : bond        0.02790 (  390)
  hydrogen bonds       : angle       4.76240 ( 1086)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.9276 (t70) cc_final: 0.9007 (t70)
REVERT: A   62 MET cc_start: 0.9324 (mpp) cc_final: 0.9101 (mpp)
REVERT: A   87 PHE cc_start: 0.9470 (m-10) cc_final: 0.8883 (m-80)
REVERT: A  135 MET cc_start: 0.9282 (mpp) cc_final: 0.9042 (mmt)
REVERT: A  167 MET cc_start: 0.9178 (tpp) cc_final: 0.8762 (tpp)
REVERT: A  168 LEU cc_start: 0.9830 (tp) cc_final: 0.9533 (tp)
REVERT: A  203 MET cc_start: 0.8179 (mpp) cc_final: 0.7920 (mtt)
REVERT: A  279 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8384 (mmtt)
REVERT: A  348 MET cc_start: 0.9147 (mmp) cc_final: 0.8495 (mmm)
REVERT: A  434 LEU cc_start: 0.9320 (tp) cc_final: 0.9100 (tp)
REVERT: A  496 ASP cc_start: 0.9271 (t0) cc_final: 0.9029 (t0)
REVERT: A  514 MET cc_start: 0.9224 (ptt) cc_final: 0.8637 (ppp)
REVERT: B   14 MET cc_start: 0.8015 (mmp) cc_final: 0.7329 (mmm)
REVERT: B   20 MET cc_start: 0.7342 (mmp) cc_final: 0.6835 (mmm)
REVERT: B  212 MET cc_start: 0.9507 (mmp) cc_final: 0.9306 (mmm)
REVERT: B  389 MET cc_start: 0.8603 (tpp) cc_final: 0.8081 (mmm)
REVERT: B  461 MET cc_start: 0.8866 (ttt) cc_final: 0.8121 (ttt)
REVERT: B  495 LEU cc_start: 0.9723 (tt) cc_final: 0.9396 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0841
  time to fit residues: 7.9858
Evaluate side-chains
  54 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0870
   chunk 20 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 101 optimal weight:    0.0060
   chunk 99 optimal weight:    0.0470
   chunk 91 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.3872

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN
** B 492 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 = 0.3090 r_free = 0.3090 target = 0.039340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.030364 restraints weight = 81665.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.031343 restraints weight = 49414.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.032027 restraints weight = 35400.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.032501 restraints weight = 28083.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.032822 restraints weight = 23939.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   9714  Z= 0.095
  Angle     :  0.502   7.654  13233  Z= 0.259
  Chirality :  0.041   0.163   1483
  Planarity :  0.003   0.040   1615
  Dihedral  : 17.222 149.303   1495
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.27), residues: 1112
  helix:  2.00 (0.27), residues: 383
  sheet: -0.65 (0.36), residues: 184
  loop :  0.20 (0.30), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.009   0.001   TYR A 400 
 PHE   0.008   0.001   PHE B 365 
 TRP   0.005   0.001   TRP C  82 
 HIS   0.002   0.000   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 9714)
  covalent geometry    : angle       0.50244 (13233)
  hydrogen bonds       : bond        0.02663 (  390)
  hydrogen bonds       : angle       4.62471 ( 1086)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1387.00 seconds
wall clock time: 24 minutes 55.26 seconds (1495.26 seconds total)