Starting phenix.real_space_refine
on Sat Sep 12 21:03:11 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/5g2x_3331/09_2026/5g2x_3331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5g2x_3331/09_2026/5g2x_3331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/5g2x_3331/09_2026/5g2x_3331.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/5g2x_3331/09_2026/5g2x_3331.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5g2x_3331/09_2026/5g2x_3331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5g2x_3331/09_2026/5g2x_3331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5g2x_3331/09_2026/5g2x_3331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5g2x_3331/09_2026/5g2x_3331.cif"
  }
  resolution = 3.8
  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=   0.001 sd=   0.006
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     703      5.49       5
     S      19      5.16       5
     C    9320      2.51       5
     N    3467      2.21       5
     O    5563      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 19072
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 14825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 692, 14825
          Classifications: {'RNAv2': 692}
          Modifications used: {'rna2p_pur': 64, 'rna2p_pyr': 34, 'rna3p_pur': 345, 'rna3p_pyr': 249}
          Link IDs: {'rna2p': 97, 'rna3p': 594}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 250
          Classifications: {'RNAv2': 12}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 1, 'rna3p': 10}
    Chain: "C"
      Number of atoms: 3997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 487, 3997
          Classifications: {'peptide': 487}
          Link IDs: {'CIS': 24, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 447}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 4.51, per 1000 atoms: 0.24
  Number of scatterers: 19072
  At special positions: 0
  Unit cell: (156.785, 152.865, 139.8, 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      19     16.00
     P     703     15.00
     O    5563      8.00
     N    3467      7.00
     C    9320      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 383.4 milliseconds
  

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  918

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 0 sheets defined
      36.6% alpha, 0.0% beta
      42 base pairs and 325 stacking pairs defined.
    Time for finding SS restraints: 2.61
  Creating SS restraints...
    Processing helix  chain 'C' and resid 5 through 13
      removed outlier: 4.153A  pdb=" N   GLU C   9 " --> pdb=" O   MET C   5 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ARG C  10 " --> pdb=" O   ALA C   6 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ILE C  11 " --> pdb=" O   ILE C   7 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER C  12 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LYS C  13 " --> pdb=" O   GLU C   9 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 5 through 13'
    Processing helix  chain 'C' and resid 30 through 41
      removed outlier: 4.746A  pdb=" N   ASP C  34 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   ILE C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   TYR C  36 " --> pdb=" O   ARG C  32 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL C  38 " --> pdb=" O   ASP C  34 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   TYR C  40 " --> pdb=" O   TYR C  36 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   GLN C  41 " --> pdb=" O   TYR C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 73
      removed outlier: 3.559A  pdb=" N   GLN C  72 " --> pdb=" O   LYS C  68 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 68 through 73'
    Processing helix  chain 'C' and resid 106 through 121
      removed outlier: 3.807A  pdb=" N   ILE C 110 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLN C 111 " --> pdb=" O   ASP C 107 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLU C 112 " --> pdb=" O   LYS C 108 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ALA C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG C 115 " --> pdb=" O   GLN C 111 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   ILE C 116 " --> pdb=" O   GLU C 112 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ILE C 117 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE C 121 " --> pdb=" O   ILE C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 148
      removed outlier: 4.273A  pdb=" N   LYS C 144 " --> pdb=" O   HIS C 140 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   THR C 145 " --> pdb=" O   THR C 141 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE C 146 " --> pdb=" O   ALA C 142 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   LYS C 147 " --> pdb=" O   LEU C 143 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ARG C 148 " --> pdb=" O   LYS C 144 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 140 through 148'
    Processing helix  chain 'C' and resid 171 through 179
      removed outlier: 4.416A  pdb=" N   ILE C 177 " --> pdb=" O   LEU C 173 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ASN C 178 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   LEU C 179 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 197
      removed outlier: 7.577A  pdb=" N   TYR C 191 " --> pdb=" O   SER C 187 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   LYS C 192 " --> pdb=" O   GLN C 188 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   PHE C 193 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LEU C 194 " --> pdb=" O   ILE C 190 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LYS C 195 " --> pdb=" O   TYR C 191 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   ALA C 196 " --> pdb=" O   LYS C 192 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   GLY C 197 " --> pdb=" O   PHE C 193 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 187 through 197'
    Processing helix  chain 'C' and resid 217 through 248
      removed outlier: 3.815A  pdb=" N   ASN C 223 " --> pdb=" O   PRO C 219 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ILE C 224 " --> pdb=" O   LEU C 220 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU C 226 " --> pdb=" O   ALA C 222 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU C 229 " --> pdb=" O   TYR C 225 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASP C 230 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LYS C 231 " --> pdb=" O   HIS C 227 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   PHE C 232 " --> pdb=" O   GLU C 228 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   VAL C 233 " --> pdb=" O   LEU C 229 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN C 235 " --> pdb=" O   LYS C 231 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   LEU C 236 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS C 237 " --> pdb=" O   VAL C 233 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LYS C 239 " --> pdb=" O   GLN C 235 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASP C 241 " --> pdb=" O   LYS C 237 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   ARG C 242 " --> pdb=" O   MET C 238 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   GLU C 243 " --> pdb=" O   LYS C 239 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   SER C 244 " --> pdb=" O   PHE C 240 " (cutoff:3.500A)
      Proline residue:  C 245  - end of helix
      removed outlier: 4.466A  pdb=" N   ILE C 248 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 331
      removed outlier: 3.874A  pdb=" N   GLN C 322 " --> pdb=" O   LYS C 318 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   TRP C 323 " --> pdb=" O   GLU C 319 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   ILE C 324 " --> pdb=" O   ASP C 320 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   LYS C 325 " --> pdb=" O   CYS C 321 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLU C 326 " --> pdb=" O   GLN C 322 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU C 328 " --> pdb=" O   ILE C 324 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   LYS C 329 " --> pdb=" O   LYS C 325 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE C 331 " --> pdb=" O   GLN C 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 343
      No H-bonds generated for 'chain 'C' and resid 341 through 343'
    Processing helix  chain 'C' and resid 393 through 400
      removed outlier: 4.603A  pdb=" N   PHE C 397 " --> pdb=" O   LYS C 393 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   ILE C 398 " --> pdb=" O   ILE C 394 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   PHE C 399 " --> pdb=" O   ARG C 395 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 425 through 440
      removed outlier: 3.952A  pdb=" N   ILE C 429 " --> pdb=" O   ASP C 425 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE C 431 " --> pdb=" O   GLU C 427 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR C 432 " --> pdb=" O   ILE C 428 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG C 437 " --> pdb=" O   ASN C 433 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   GLY C 438 " --> pdb=" O   SER C 434 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   ILE C 439 " --> pdb=" O   GLU C 435 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   CYS C 440 " --> pdb=" O   LEU C 436 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 450 through 470
      removed outlier: 3.550A  pdb=" N   ALA C 456 " --> pdb=" O   LEU C 452 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   TYR C 457 " --> pdb=" O   ASN C 453 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   LEU C 458 " --> pdb=" O   TYR C 454 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   MET C 459 " --> pdb=" O   PHE C 455 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   TYR C 461 " --> pdb=" O   TYR C 457 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   SER C 462 " --> pdb=" O   LEU C 458 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   CYS C 463 " --> pdb=" O   MET C 459 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU C 464 " --> pdb=" O   GLU C 460 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR C 466 " --> pdb=" O   SER C 462 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE C 467 " --> pdb=" O   CYS C 463 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS C 470 " --> pdb=" O   THR C 466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 529 through 538
      removed outlier: 4.339A  pdb=" N   THR C 533 " --> pdb=" O   TYR C 529 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LEU C 534 " --> pdb=" O   ALA C 530 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU C 535 " --> pdb=" O   ARG C 531 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ARG C 537 " --> pdb=" O   THR C 533 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LEU C 538 " --> pdb=" O   LEU C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 552 through 553
      No H-bonds generated for 'chain 'C' and resid 552 through 553'

    31 hydrogen bonds defined for protein.
    93 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      89 hydrogen bonds
      154 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      325 stacking parallelities
  Total time for adding SS restraints: 4.12

  Time building geometry restraints manager: 2.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3171
        1.34 -     1.45: 9106
        1.45 -     1.57: 7265
        1.57 -     1.69: 1402
        1.69 -     1.81: 28
  Bond restraints: 20972
  Sorted by residual:
  bond pdb=" C   HIS C 591 "
       pdb=" N   ARG C 592 "
    ideal  model  delta    sigma   weight residual
    1.329  1.231  0.098 1.40e-02 5.10e+03 4.87e+01
  bond pdb=" CA  ASN C  18 "
       pdb=" C   ASN C  18 "
    ideal  model  delta    sigma   weight residual
    1.523  1.554 -0.031 1.34e-02 5.57e+03 5.28e+00
  bond pdb=" CA  TYR C 527 "
       pdb=" C   TYR C 527 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.032 1.40e-02 5.10e+03 5.15e+00
  bond pdb=" CA  TYR C  44 "
       pdb=" C   TYR C  44 "
    ideal  model  delta    sigma   weight residual
    1.524  1.547 -0.024 1.26e-02 6.30e+03 3.53e+00
  bond pdb=" CA  ASN C  46 "
       pdb=" C   ASN C  46 "
    ideal  model  delta    sigma   weight residual
    1.524  1.546 -0.023 1.26e-02 6.30e+03 3.23e+00
  ... (remaining 20967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 29867
        2.20 -     4.40: 1789
        4.40 -     6.60: 144
        6.60 -     8.79: 3
        8.79 -    10.99: 1
  Bond angle restraints: 31804
  Sorted by residual:
  angle pdb=" C   ASN C  18 "
        pdb=" N   ILE C  19 "
        pdb=" CA  ILE C  19 "
      ideal   model   delta    sigma   weight residual
     121.70  132.69  -10.99 1.80e+00 3.09e-01 3.73e+01
  angle pdb=" C3'   G A 559 "
        pdb=" O3'   G A 559 "
        pdb=" P     A A 560 "
      ideal   model   delta    sigma   weight residual
     119.70  125.08   -5.38 1.20e+00 6.94e-01 2.01e+01
  angle pdb=" C3'   A A 149 "
        pdb=" O3'   A A 149 "
        pdb=" P     C A 150 "
      ideal   model   delta    sigma   weight residual
     119.70  125.07   -5.37 1.20e+00 6.94e-01 2.00e+01
  angle pdb=" CA  ASN C  18 "
        pdb=" C   ASN C  18 "
        pdb=" N   ILE C  19 "
      ideal   model   delta    sigma   weight residual
     116.84  124.40   -7.56 1.71e+00 3.42e-01 1.95e+01
  angle pdb=" C   VAL C 375 "
        pdb=" N   LYS C 376 "
        pdb=" CA  LYS C 376 "
      ideal   model   delta    sigma   weight residual
     121.70  129.32   -7.62 1.80e+00 3.09e-01 1.79e+01
  ... (remaining 31799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.70: 9707
       34.70 -    69.39: 1099
       69.39 -   104.09: 97
      104.09 -   138.78: 0
      138.78 -   173.48: 6
  Dihedral angle restraints: 10909
    sinusoidal: 9481
      harmonic: 1428
  Sorted by residual:
  dihedral pdb=" C4'   A A 546 "
           pdb=" C3'   A A 546 "
           pdb=" C2'   A A 546 "
           pdb=" C1'   A A 546 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.89   73.23     1      3.10e+00 1.04e-01 7.11e+02
  dihedral pdb=" C4'   C A 251 "
           pdb=" C3'   C A 251 "
           pdb=" C2'   C A 251 "
           pdb=" C1'   C A 251 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -36.15   72.50     1      3.10e+00 1.04e-01 6.99e+02
  dihedral pdb=" C4'   G A 146 "
           pdb=" C3'   G A 146 "
           pdb=" C2'   G A 146 "
           pdb=" C1'   G A 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.12   72.46     1      3.10e+00 1.04e-01 6.98e+02
  ... (remaining 10906 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 3159
       0.072 -    0.144: 52
       0.144 -    0.216: 6
       0.216 -    0.287: 889
       0.287 -    0.359: 8
  Chirality restraints: 4114
  Sorted by residual:
  chirality pdb=" P     A A 560 "
            pdb=" OP1   A A 560 "
            pdb=" OP2   A A 560 "
            pdb=" O5'   A A 560 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17    2.53   -0.36 2.00e-01 2.50e+01 3.23e+00
  chirality pdb=" P     C A 150 "
            pdb=" OP1   C A 150 "
            pdb=" OP2   C A 150 "
            pdb=" O5'   C A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.52   -0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" P     A A 178 "
            pdb=" OP1   A A 178 "
            pdb=" OP2   A A 178 "
            pdb=" O5'   A A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.51   -0.33 2.00e-01 2.50e+01 2.75e+00
  ... (remaining 4111 not shown)

  Planarity restraints: 1389
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 123 "    0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO C 124 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C 124 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 124 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 218 "   -0.014 5.00e-02 4.00e+02   2.12e-02 7.21e-01
        pdb=" N   PRO C 219 "    0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO C 219 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO C 219 "   -0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 211 "   -0.013 5.00e-02 4.00e+02   1.96e-02 6.16e-01
        pdb=" N   PRO C 212 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO C 212 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO C 212 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 1386 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2529
        2.76 -     3.29: 15686
        3.29 -     3.83: 33394
        3.83 -     4.36: 40872
        4.36 -     4.90: 54857
  Nonbonded interactions: 147338
  Sorted by model distance:
  nonbonded pdb=" O2'   C B   1 "
            pdb=" O4'   A B   2 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O2'   C A2395 "
            pdb=" O5'   A A2396 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O2'   C A   7 "
            pdb=" O2'   A A 516 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ARG C  25 "
            pdb=" OH  TYR C  29 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OP2   A A 563 "
            pdb=" OH  TYR C  36 "
     model   vdw
     2.295 3.040
  ... (remaining 147333 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:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     20.920
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2984
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   0.098  20972  Z= 0.140
  Angle     :  0.842  10.992  31804  Z= 0.358
  Chirality :  0.115   0.359   4114
  Planarity :  0.002   0.046   1389
  Dihedral  : 19.206 173.479   9991
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  5.88 %
    Allowed  : 19.75 %
    Favored  : 74.37 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  1.59 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -5.72 (0.28), residues: 476
  helix: -4.59 (0.17), residues: 102
  sheet: -4.08 (1.23), residues: 9
  loop : -3.91 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 154 
 TYR   0.007   0.000   TYR C 204 
 PHE   0.003   0.000   PHE C 156 
 TRP   0.003   0.000   TRP C 202 
 HIS   0.001   0.000   HIS C 131 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.14 (20972)
  covalent geometry    : angle       0.84171 /  0.36 (31804)
  hydrogen bonds       : bond        0.32553 / 16.85 (  120)
  hydrogen bonds       : angle      12.98927 /  4.97 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  481 MET cc_start: 0.5012 (mmt) cc_final: 0.4804 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 124
  average time/residue: 0.1563
  time to fit residues: 28.2385
Evaluate side-chains
  65 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  390 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  82 GLN
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 203 GLN
C 213 GLN
C 223 ASN
C 381 ASN
** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.131935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.114758 restraints weight = 117712.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.116420 restraints weight = 69759.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.116206 restraints weight = 48586.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.116612 restraints weight = 48317.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.116643 restraints weight = 38366.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6006
moved from start:          0.5611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.070  20972  Z= 0.381
  Angle     :  1.673  17.066  31804  Z= 0.653
  Chirality :  0.109   1.099   4114
  Planarity :  0.006   0.054   1389
  Dihedral  : 19.477 176.729   8971
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 27.79
  Ramachandran Plot:
    Outliers :  1.26 %
    Allowed  : 18.70 %
    Favored  : 80.04 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 10.43 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -5.06 (0.30), residues: 476
  helix: -2.89 (0.34), residues: 121
  sheet:  None (None), residues: 0
  loop : -3.89 (0.27), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 437 
 TYR   0.027   0.004   TYR C 306 
 PHE   0.025   0.003   PHE C 310 
 TRP   0.016   0.003   TRP C 412 
 HIS   0.011   0.002   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00761 /  0.38 (20972)
  covalent geometry    : angle       1.67296 /  0.65 (31804)
  hydrogen bonds       : bond        0.15313 /  8.07 (  120)
  hydrogen bonds       : angle       4.81049 /  1.98 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   22 VAL cc_start: 0.1608 (m) cc_final: 0.1217 (m)
REVERT: C  108 LYS cc_start: 0.7087 (mtmm) cc_final: 0.6398 (tmtt)
REVERT: C  155 TRP cc_start: 0.3663 (m-10) cc_final: 0.3314 (m-10)
REVERT: C  306 TYR cc_start: 0.4689 (m-80) cc_final: 0.4415 (m-80)
REVERT: C  342 GLU cc_start: 0.6045 (pm20) cc_final: 0.5806 (pm20)
REVERT: C  499 LYS cc_start: 0.3647 (tptp) cc_final: 0.1579 (tttt)
  outliers start: 16
  outliers final: 7
  residues processed: 86
  average time/residue: 0.1504
  time to fit residues: 19.6354
Evaluate side-chains
  59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  167 ASN
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  431 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 62 optimal weight:    0.5980
   chunk 59 optimal weight:    6.9990
   overall best weight:    3.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  93 ASN
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 223 ASN
** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 497 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.128082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.110012 restraints weight = 116991.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.111260 restraints weight = 63457.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.112058 restraints weight = 42837.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.111904 restraints weight = 38549.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.111927 restraints weight = 34541.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6198
moved from start:          0.7344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  20972  Z= 0.256
  Angle     :  1.219  13.622  31804  Z= 0.485
  Chirality :  0.084   0.529   4114
  Planarity :  0.005   0.066   1389
  Dihedral  : 19.574 173.246   8969
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 21.74
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 18.70 %
    Favored  : 80.25 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.87 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -4.57 (0.33), residues: 476
  helix: -2.01 (0.45), residues: 119
  sheet:  None (None), residues: 0
  loop : -3.75 (0.28), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 437 
 TYR   0.022   0.003   TYR C 225 
 PHE   0.012   0.002   PHE C 356 
 TRP   0.008   0.002   TRP C 412 
 HIS   0.008   0.002   HIS C 349 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00518 /  0.26 (20972)
  covalent geometry    : angle       1.21890 /  0.49 (31804)
  hydrogen bonds       : bond        0.12459 /  7.11 (  120)
  hydrogen bonds       : angle       4.32259 /  1.75 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  342 GLU cc_start: 0.5949 (pm20) cc_final: 0.5577 (pm20)
REVERT: C  442 TYR cc_start: 0.4307 (m-80) cc_final: 0.4107 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 69
  average time/residue: 0.1309
  time to fit residues: 14.5968
Evaluate side-chains
  55 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  167 ASN
Chi-restraints excluded: chain C residue  244 SER
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  405 ILE
Chi-restraints excluded: chain C residue  424 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 104 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 67 optimal weight:   30.0000
   chunk 111 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 105 optimal weight:    5.9990
   overall best weight:    4.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 203 GLN
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 406 GLN
** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 536 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.118757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.097957 restraints weight = 110923.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.099881 restraints weight = 59878.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.099872 restraints weight = 39540.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.100225 restraints weight = 33096.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.100406 restraints weight = 28271.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6466
moved from start:          0.9520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093  20972  Z= 0.315
  Angle     :  1.394  16.142  31804  Z= 0.551
  Chirality :  0.091   0.788   4114
  Planarity :  0.006   0.056   1389
  Dihedral  : 20.198 178.579   8969
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 28.77
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 19.96 %
    Favored  : 78.99 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 17.01 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -4.83 (0.32), residues: 476
  helix: -2.30 (0.38), residues: 140
  sheet:  None (None), residues: 0
  loop : -3.95 (0.28), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 355 
 TYR   0.036   0.004   TYR C 225 
 PHE   0.032   0.003   PHE C 310 
 TRP   0.010   0.002   TRP C 323 
 HIS   0.011   0.002   HIS C 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00639 /  0.32 (20972)
  covalent geometry    : angle       1.39380 /  0.55 (31804)
  hydrogen bonds       : bond        0.14121 /  7.89 (  120)
  hydrogen bonds       : angle       4.78798 /  1.96 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 62
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  134 ARG cc_start: 0.6995 (mmt90) cc_final: 0.6760 (mmm160)
REVERT: C  226 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8094 (tp)
REVERT: C  386 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4573 (pp)
REVERT: C  459 MET cc_start: 0.7094 (mmm) cc_final: 0.6781 (mmm)
REVERT: C  480 SER cc_start: 0.5407 (p) cc_final: 0.4946 (t)
REVERT: C  481 MET cc_start: 0.5895 (mmt) cc_final: 0.5456 (mmm)
REVERT: C  500 GLN cc_start: 0.3546 (OUTLIER) cc_final: 0.3060 (tt0)
  outliers start: 25
  outliers final: 15
  residues processed: 83
  average time/residue: 0.1361
  time to fit residues: 17.7243
Evaluate side-chains
  70 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 52
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  167 ASN
Chi-restraints excluded: chain C residue  176 LEU
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  244 SER
Chi-restraints excluded: chain C residue  304 VAL
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  331 PHE
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  405 ILE
Chi-restraints excluded: chain C residue  500 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 69 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 41 optimal weight:   40.0000
   chunk 50 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    3.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 433 ASN
** C 451 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 = 0.4495 r_free = 0.4495 target = 0.119393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.099291 restraints weight = 108802.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.101309 restraints weight = 57142.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.101130 restraints weight = 34403.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.101406 restraints weight = 28812.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.101724 restraints weight = 25369.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
moved from start:          1.0060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  20972  Z= 0.251
  Angle     :  1.228  15.506  31804  Z= 0.488
  Chirality :  0.083   0.609   4114
  Planarity :  0.006   0.095   1389
  Dihedral  : 20.243 174.911   8969
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 22.85
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 17.02 %
    Favored  : 81.93 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 20.41 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -4.84 (0.32), residues: 476
  helix: -2.17 (0.39), residues: 142
  sheet:  None (None), residues: 0
  loop : -4.04 (0.27), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 355 
 TYR   0.027   0.003   TYR C 225 
 PHE   0.027   0.003   PHE C  23 
 TRP   0.008   0.002   TRP C 323 
 HIS   0.009   0.002   HIS C 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00506 /  0.25 (20972)
  covalent geometry    : angle       1.22816 /  0.49 (31804)
  hydrogen bonds       : bond        0.11846 /  6.47 (  120)
  hydrogen bonds       : angle       4.44973 /  1.75 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.6907 (m-80) cc_final: 0.6309 (t80)
REVERT: C  184 MET cc_start: 0.7698 (ptt) cc_final: 0.7166 (pmm)
REVERT: C  481 MET cc_start: 0.5650 (mmt) cc_final: 0.5308 (mmm)
REVERT: C  494 GLU cc_start: 0.1174 (OUTLIER) cc_final: 0.0571 (pm20)
REVERT: C  500 GLN cc_start: 0.3403 (OUTLIER) cc_final: 0.2902 (tt0)
  outliers start: 20
  outliers final: 9
  residues processed: 72
  average time/residue: 0.1415
  time to fit residues: 15.9748
Evaluate side-chains
  59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  172 THR
Chi-restraints excluded: chain C residue  331 PHE
Chi-restraints excluded: chain C residue  393 LYS
Chi-restraints excluded: chain C residue  405 ILE
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain C residue  500 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 43 optimal weight:   30.0000
   chunk 72 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   chunk 0 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 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 = 0.4491 r_free = 0.4491 target = 0.119122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.099942 restraints weight = 109242.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.100656 restraints weight = 54711.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.101142 restraints weight = 50707.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.101273 restraints weight = 41743.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.101392 restraints weight = 38403.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6332
moved from start:          1.0438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  20972  Z= 0.224
  Angle     :  1.190  14.297  31804  Z= 0.472
  Chirality :  0.081   0.621   4114
  Planarity :  0.005   0.052   1389
  Dihedral  : 20.225 178.172   8969
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 21.77
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 18.07 %
    Favored  : 81.09 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 20.63 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -4.53 (0.33), residues: 476
  helix: -1.81 (0.43), residues: 130
  sheet:  None (None), residues: 0
  loop : -3.83 (0.28), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 355 
 TYR   0.022   0.002   TYR C 225 
 PHE   0.016   0.002   PHE C  23 
 TRP   0.007   0.002   TRP C 155 
 HIS   0.009   0.002   HIS C 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.22 (20972)
  covalent geometry    : angle       1.18979 /  0.47 (31804)
  hydrogen bonds       : bond        0.11881 /  6.41 (  120)
  hydrogen bonds       : angle       4.32058 /  1.69 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.6861 (m-80) cc_final: 0.6290 (t80)
REVERT: C  109 LEU cc_start: 0.6495 (mt) cc_final: 0.6157 (mt)
REVERT: C  452 LEU cc_start: 0.8207 (tp) cc_final: 0.7817 (tt)
REVERT: C  481 MET cc_start: 0.5846 (mmt) cc_final: 0.5381 (mmm)
REVERT: C  494 GLU cc_start: 0.1172 (OUTLIER) cc_final: 0.0300 (pm20)
REVERT: C  500 GLN cc_start: 0.3435 (OUTLIER) cc_final: 0.2872 (tt0)
  outliers start: 19
  outliers final: 12
  residues processed: 70
  average time/residue: 0.1489
  time to fit residues: 16.1960
Evaluate side-chains
  64 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  331 PHE
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  405 ILE
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain C residue  500 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 40 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 349 HIS
** C 451 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 = 0.4449 r_free = 0.4449 target = 0.116108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.095444 restraints weight = 106047.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.097546 restraints weight = 51280.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.097334 restraints weight = 39571.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.097409 restraints weight = 33234.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.099317 restraints weight = 28965.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          1.1295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  20972  Z= 0.303
  Angle     :  1.341  14.842  31804  Z= 0.532
  Chirality :  0.088   0.648   4114
  Planarity :  0.007   0.099   1389
  Dihedral  : 20.574 179.337   8969
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 28.38
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 19.33 %
    Favored  : 79.83 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 22.45 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -4.85 (0.32), residues: 476
  helix: -2.30 (0.40), residues: 139
  sheet:  None (None), residues: 0
  loop : -3.97 (0.27), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.002   ARG C 537 
 TYR   0.038   0.003   TYR C 529 
 PHE   0.029   0.004   PHE C  23 
 TRP   0.019   0.003   TRP C 323 
 HIS   0.011   0.002   HIS C 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00610 /  0.30 (20972)
  covalent geometry    : angle       1.34147 /  0.53 (31804)
  hydrogen bonds       : bond        0.13841 /  7.34 (  120)
  hydrogen bonds       : angle       4.98722 /  1.95 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.6904 (m-80) cc_final: 0.6096 (t80)
REVERT: C  109 LEU cc_start: 0.6843 (mt) cc_final: 0.6546 (mt)
REVERT: C  134 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6120 (mmm160)
REVERT: C  238 MET cc_start: 0.6779 (mtt) cc_final: 0.6460 (mtt)
REVERT: C  380 LEU cc_start: 0.6838 (mp) cc_final: 0.6369 (mt)
REVERT: C  426 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6937 (mm)
REVERT: C  481 MET cc_start: 0.5841 (mmt) cc_final: 0.5336 (mmm)
REVERT: C  494 GLU cc_start: 0.1892 (OUTLIER) cc_final: 0.0985 (pm20)
REVERT: C  500 GLN cc_start: 0.3429 (OUTLIER) cc_final: 0.2948 (tt0)
  outliers start: 17
  outliers final: 12
  residues processed: 66
  average time/residue: 0.1468
  time to fit residues: 15.0253
Evaluate side-chains
  64 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  134 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  331 PHE
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  393 LYS
Chi-restraints excluded: chain C residue  405 ILE
Chi-restraints excluded: chain C residue  426 LEU
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain C residue  500 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 83 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 107 optimal weight:    0.9990
   chunk 84 optimal weight:    0.2980
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 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 = 0.4536 r_free = 0.4536 target = 0.124132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.106493 restraints weight = 116191.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.107896 restraints weight = 58226.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.108171 restraints weight = 44486.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.108271 restraints weight = 39600.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.108278 restraints weight = 34019.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6261
moved from start:          1.1051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  20972  Z= 0.168
  Angle     :  1.097  13.749  31804  Z= 0.439
  Chirality :  0.076   0.560   4114
  Planarity :  0.005   0.049   1389
  Dihedral  : 20.241 178.918   8969
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 16.39 %
    Favored  : 82.77 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 25.62 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -4.72 (0.31), residues: 476
  helix: -2.14 (0.39), residues: 139
  sheet:  None (None), residues: 0
  loop : -3.91 (0.27), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.033   0.001   ARG C 355 
 TYR   0.017   0.002   TYR C 225 
 PHE   0.019   0.002   PHE C 133 
 TRP   0.013   0.002   TRP C 323 
 HIS   0.009   0.001   HIS C 349 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.17 (20972)
  covalent geometry    : angle       1.09688 /  0.44 (31804)
  hydrogen bonds       : bond        0.10004 /  5.23 (  120)
  hydrogen bonds       : angle       4.19131 /  1.65 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.7168 (m-80) cc_final: 0.6192 (t80)
REVERT: C  134 ARG cc_start: 0.7093 (mmp-170) cc_final: 0.5730 (mmm160)
REVERT: C  176 LEU cc_start: 0.8142 (mm) cc_final: 0.7838 (mm)
REVERT: C  380 LEU cc_start: 0.6680 (mp) cc_final: 0.6247 (mt)
  outliers start: 8
  outliers final: 7
  residues processed: 58
  average time/residue: 0.1539
  time to fit residues: 13.7272
Evaluate side-chains
  50 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  331 PHE
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  424 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 44 optimal weight:   30.0000
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 78 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0170
   chunk 40 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   chunk 91 optimal weight:    8.9990
   chunk 66 optimal weight:   40.0000
   chunk 56 optimal weight:    9.9990
   overall best weight:    5.1224

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 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 = 0.4439 r_free = 0.4439 target = 0.115604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.095066 restraints weight = 104880.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.097358 restraints weight = 50801.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.097366 restraints weight = 33249.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.097430 restraints weight = 25507.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.097542 restraints weight = 26402.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6463
moved from start:          1.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  20972  Z= 0.312
  Angle     :  1.361  14.216  31804  Z= 0.538
  Chirality :  0.088   0.646   4114
  Planarity :  0.006   0.063   1389
  Dihedral  : 20.665 179.100   8969
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 29.19
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 20.17 %
    Favored  : 78.99 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 25.17 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -4.86 (0.31), residues: 476
  helix: -2.17 (0.41), residues: 133
  sheet:  None (None), residues: 0
  loop : -4.02 (0.26), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  32 
 TYR   0.032   0.003   TYR C 225 
 PHE   0.020   0.004   PHE C 356 
 TRP   0.017   0.003   TRP C 323 
 HIS   0.019   0.002   HIS C 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00632 /  0.31 (20972)
  covalent geometry    : angle       1.36127 /  0.54 (31804)
  hydrogen bonds       : bond        0.13878 /  7.27 (  120)
  hydrogen bonds       : angle       4.83040 /  1.84 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.7367 (m-80) cc_final: 0.6278 (t80)
REVERT: C  134 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.5980 (mmm160)
REVERT: C  176 LEU cc_start: 0.8398 (mm) cc_final: 0.8101 (mm)
REVERT: C  380 LEU cc_start: 0.7192 (mp) cc_final: 0.6941 (mt)
REVERT: C  426 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7044 (mm)
REVERT: C  500 GLN cc_start: 0.3605 (OUTLIER) cc_final: 0.3140 (tt0)
  outliers start: 11
  outliers final: 8
  residues processed: 58
  average time/residue: 0.1374
  time to fit residues: 12.2957
Evaluate side-chains
  54 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue  134 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  306 TYR
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  331 PHE
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  426 LEU
Chi-restraints excluded: chain C residue  500 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 58 optimal weight:   20.0000
   chunk 89 optimal weight:    0.2980
   chunk 51 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 110 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    1.8186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 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 = 0.4522 r_free = 0.4522 target = 0.123122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.105389 restraints weight = 115871.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.106860 restraints weight = 58586.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.106572 restraints weight = 50998.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.106917 restraints weight = 44763.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.106964 restraints weight = 37380.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6306
moved from start:          1.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  20972  Z= 0.175
  Angle     :  1.124  16.104  31804  Z= 0.448
  Chirality :  0.077   0.550   4114
  Planarity :  0.006   0.108   1389
  Dihedral  : 20.421 179.622   8969
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 16.39 %
    Favored  : 82.56 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 26.08 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -4.84 (0.31), residues: 476
  helix: -2.12 (0.40), residues: 133
  sheet: -3.80 (1.48), residues: 10
  loop : -4.00 (0.27), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 537 
 TYR   0.017   0.002   TYR C 225 
 PHE   0.011   0.002   PHE C 133 
 TRP   0.012   0.002   TRP C 412 
 HIS   0.011   0.002   HIS C 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.17 (20972)
  covalent geometry    : angle       1.12388 /  0.45 (31804)
  hydrogen bonds       : bond        0.10512 /  5.52 (  120)
  hydrogen bonds       : angle       4.28625 /  1.66 (  247)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.7071 (m-80) cc_final: 0.6187 (t80)
REVERT: C  134 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.5860 (mmm160)
REVERT: C  176 LEU cc_start: 0.8154 (mm) cc_final: 0.7824 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1372
  time to fit residues: 12.2001
Evaluate side-chains
  50 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue  134 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  172 THR
Chi-restraints excluded: chain C residue  324 ILE
Chi-restraints excluded: chain C residue  331 PHE
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  424 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 64 optimal weight:   20.0000
   chunk 105 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 68 optimal weight:    9.9990
   chunk 107 optimal weight:    0.0010
   chunk 117 optimal weight:    0.2980
   chunk 46 optimal weight:    6.9990
   chunk 101 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   overall best weight:    2.8190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 223 ASN
** C 451 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 = 0.4490 r_free = 0.4490 target = 0.118886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.099951 restraints weight = 107873.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.100962 restraints weight = 51726.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.101437 restraints weight = 40120.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.101478 restraints weight = 36239.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.101479 restraints weight = 33244.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6353
moved from start:          1.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  20972  Z= 0.203
  Angle     :  1.162  16.904  31804  Z= 0.462
  Chirality :  0.078   0.588   4114
  Planarity :  0.006   0.103   1389
  Dihedral  : 20.472 179.637   8969
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 22.55
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 18.49 %
    Favored  : 80.67 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 26.30 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 5.15 %
    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: -4.80 (0.32), residues: 476
  helix: -2.20 (0.40), residues: 137
  sheet: -4.07 (1.30), residues: 10
  loop : -3.92 (0.29), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 537 
 TYR   0.025   0.002   TYR C 225 
 PHE   0.015   0.002   PHE C  23 
 TRP   0.012   0.002   TRP C 412 
 HIS   0.016   0.002   HIS C 170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.20 (20972)
  covalent geometry    : angle       1.16219 /  0.46 (31804)
  hydrogen bonds       : bond        0.11155 /  5.93 (  120)
  hydrogen bonds       : angle       4.51750 /  1.73 (  247)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2989.68 seconds
wall clock time: 52 minutes 43.19 seconds (3163.19 seconds total)