Starting phenix.real_space_refine
on Sat Aug 23 18:04:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iqg_35661/08_2025/8iqg_35661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iqg_35661/08_2025/8iqg_35661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iqg_35661/08_2025/8iqg_35661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iqg_35661/08_2025/8iqg_35661.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iqg_35661/08_2025/8iqg_35661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iqg_35661/08_2025/8iqg_35661.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6634 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5428      2.51       5
     N    1537      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8517
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1439
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 11, 'TRANS': 201}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 306
          Unresolved non-hydrogen angles: 385
          Unresolved non-hydrogen dihedrals: 252
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ASP:plan': 17, 'GLN:plan1': 8, 'GLU:plan': 12, 'ARG:plan': 6, 'TRP:plan': 2, 'PHE:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 210
    Chain: "D"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 833
          Classifications: {'peptide': 110}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 37
    Chain: "E"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 612
          Classifications: {'peptide': 79}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "C"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 2950
          Classifications: {'peptide': 401}
          Incomplete info: {'truncation_to_alanine': 76}
          Link IDs: {'PTRANS': 22, 'TRANS': 378}
          Unresolved non-hydrogen bonds: 244
          Unresolved non-hydrogen angles: 305
          Unresolved non-hydrogen dihedrals: 194
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 13, 'GLN:plan1': 3, 'PHE:plan': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 173
    Chain: "B"
      Number of atoms: 2683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2683
          Classifications: {'peptide': 365}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 15, 'TRANS': 349}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 241
          Unresolved non-hydrogen dihedrals: 155
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 9, 'ASN:plan1': 6, 'GLN:plan1': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 105
  Time building chain proxies: 1.76, per 1000 atoms: 0.21
  Number of scatterers: 8517
  At special positions: 0
  Unit cell: (79, 89, 127, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1520      8.00
     N    1537      7.00
     C    5428      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 420.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2198

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 20 sheets defined
      20.1% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 490 through 502
      removed outlier: 3.565A  pdb=" N   GLN A 500 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 514
      removed outlier: 3.664A  pdb=" N   ASP A 511 " --> pdb=" O   SER A 507 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LYS A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   GLY A 514 " --> pdb=" O   LYS A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 554
    Processing helix  chain 'A' and resid 599 through 604
    Processing helix  chain 'A' and resid 635 through 647
    Processing helix  chain 'A' and resid 652 through 675
    Processing helix  chain 'A' and resid 697 through 706
    Processing helix  chain 'D' and resid 63 through 79
      removed outlier: 3.660A  pdb=" N   PHE D  67 " --> pdb=" O   ARG D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 114
    Processing helix  chain 'D' and resid 120 through 131
    Processing helix  chain 'E' and resid 25 through 29
      removed outlier: 4.304A  pdb=" N   ILE E  29 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 40
    Processing helix  chain 'E' and resid 47 through 49
      No H-bonds generated for 'chain 'E' and resid 47 through 49'
    Processing helix  chain 'E' and resid 50 through 75
    Processing helix  chain 'E' and resid 82 through 94
    Processing helix  chain 'C' and resid 12 through 32
      Proline residue:  C  29  - end of helix
    Processing helix  chain 'C' and resid 155 through 157
      No H-bonds generated for 'chain 'C' and resid 155 through 157'
    Processing helix  chain 'C' and resid 208 through 210
      No H-bonds generated for 'chain 'C' and resid 208 through 210'
    Processing helix  chain 'C' and resid 355 through 360
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.352A  pdb=" N   TYR C 409 " --> pdb=" O   ALA C 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 572
      removed outlier: 3.521A  pdb=" N   ASP C 379 " --> pdb=" O   VAL C 393 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 686
      removed outlier: 4.084A  pdb=" N   TYR B 340 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 54
      removed outlier: 6.508A  pdb=" N   ASP C  52 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ARG C  65 " --> pdb=" O   ASP C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 83
      removed outlier: 7.356A  pdb=" N   ASN C  77 " --> pdb=" O   ASN C 122 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   ASN C 122 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   LEU C  79 " --> pdb=" O   LYS C 120 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LYS C 120 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE C  81 " --> pdb=" O   GLU C 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 132
    Processing sheet with id=AA6, first strand: chain 'C' and resid 172 through 173
      removed outlier: 6.833A  pdb=" N   ARG C 172 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 185
      removed outlier: 3.855A  pdb=" N   GLY C 182 " --> pdb=" O   ALA C 196 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 230 through 235
      removed outlier: 6.886A  pdb=" N   VAL C 246 " --> pdb=" O   GLU C 231 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL C 233 " --> pdb=" O   GLY C 244 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   GLY C 244 " --> pdb=" O   VAL C 233 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   TRP C 235 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   LEU C 242 " --> pdb=" O   TRP C 235 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA C 247 " --> pdb=" O   LYS C 251 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LYS C 251 " --> pdb=" O   ALA C 247 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   HIS C 267 " --> pdb=" O   ILE C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 279 through 281
      removed outlier: 3.834A  pdb=" N   HIS C 311 " --> pdb=" O   LEU C 300 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 320 through 323
      removed outlier: 6.766A  pdb=" N   SER C 336 " --> pdb=" O   PHE C 321 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 6
      removed outlier: 4.402A  pdb=" N   CYS B 370 " --> pdb=" O   CYS B   6 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 16 through 18
      removed outlier: 6.789A  pdb=" N   ALA B  35 " --> pdb=" O   TYR B  17 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 30 through 33
      removed outlier: 6.673A  pdb=" N   VAL B  41 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   ASN B  61 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ILE B  43 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 71
      removed outlier: 5.191A  pdb=" N   VAL B  89 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ILE B  90 " --> pdb=" O   THR B 124 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   THR B 124 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU B  92 " --> pdb=" O   VAL B 122 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR B 120 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 132 through 136
      removed outlier: 6.468A  pdb=" N   ALA B 147 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ILE B 135 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ALA B 145 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 154 through 156
      removed outlier: 6.847A  pdb=" N   ILE B 155 " --> pdb=" O   ILE B 164 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 174 through 177
      removed outlier: 3.697A  pdb=" N   PHE B 207 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   SER B 199 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   VAL B 205 " --> pdb=" O   SER B 199 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 241 through 242
      removed outlier: 3.644A  pdb=" N   LEU B 250 " --> pdb=" O   SER B 241 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   LEU B 250 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   PHE B 269 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   TYR B 267 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA B 279 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 288 through 293
      removed outlier: 6.795A  pdb=" N   ALA B 322 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   VAL B 291 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ALA B 320 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 299

    261 hydrogen bonds defined for protein.
    729 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2635
        1.33 -     1.45: 1322
        1.45 -     1.57: 4713
        1.57 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 8717
  Sorted by residual:
  bond pdb=" CG  LEU D  92 "
       pdb=" CD2 LEU D  92 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.12e+00
  bond pdb=" CB  VAL C  35 "
       pdb=" CG2 VAL C  35 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.51e-01
  bond pdb=" CG  LEU C 333 "
       pdb=" CD1 LEU C 333 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.75e-01
  bond pdb=" CG  LEU B 240 "
       pdb=" CD2 LEU B 240 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.04e-01
  bond pdb=" CA  LEU C  34 "
       pdb=" C   LEU C  34 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 7.47e-01
  ... (remaining 8712 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 11721
        1.95 -     3.89: 148
        3.89 -     5.84: 18
        5.84 -     7.78: 5
        7.78 -     9.73: 1
  Bond angle restraints: 11893
  Sorted by residual:
  angle pdb=" N   ASP C  33 "
        pdb=" CA  ASP C  33 "
        pdb=" C   ASP C  33 "
      ideal   model   delta    sigma   weight residual
     114.56  110.23    4.33 1.27e+00 6.20e-01 1.16e+01
  angle pdb=" C   PRO C 387 "
        pdb=" N   TRP C 388 "
        pdb=" CA  TRP C 388 "
      ideal   model   delta    sigma   weight residual
     121.54  127.08   -5.54 1.91e+00 2.74e-01 8.41e+00
  angle pdb=" N   GLU A 606 "
        pdb=" CA  GLU A 606 "
        pdb=" C   GLU A 606 "
      ideal   model   delta    sigma   weight residual
     110.97  114.10   -3.13 1.09e+00 8.42e-01 8.26e+00
  angle pdb=" N   THR C  28 "
        pdb=" CA  THR C  28 "
        pdb=" C   THR C  28 "
      ideal   model   delta    sigma   weight residual
     109.81  116.05   -6.24 2.21e+00 2.05e-01 7.98e+00
  angle pdb=" CA  LEU D  61 "
        pdb=" CB  LEU D  61 "
        pdb=" CG  LEU D  61 "
      ideal   model   delta    sigma   weight residual
     116.30  126.03   -9.73 3.50e+00 8.16e-02 7.73e+00
  ... (remaining 11888 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4500
       17.96 -    35.93: 487
       35.93 -    53.89: 119
       53.89 -    71.86: 16
       71.86 -    89.82: 10
  Dihedral angle restraints: 5132
    sinusoidal: 1745
      harmonic: 3387
  Sorted by residual:
  dihedral pdb=" CA  TRP A 604 "
           pdb=" C   TRP A 604 "
           pdb=" N   GLU A 605 "
           pdb=" CA  GLU A 605 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.24   18.76     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLU A 605 "
           pdb=" C   GLU A 605 "
           pdb=" N   GLU A 606 "
           pdb=" CA  GLU A 606 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CB  GLU C 124 "
           pdb=" CG  GLU C 124 "
           pdb=" CD  GLU C 124 "
           pdb=" OE1 GLU C 124 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.64  -89.64     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 5129 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 881
       0.034 -    0.069: 313
       0.069 -    0.103: 104
       0.103 -    0.138: 60
       0.138 -    0.172: 2
  Chirality restraints: 1360
  Sorted by residual:
  chirality pdb=" CA  THR C  28 "
            pdb=" N   THR C  28 "
            pdb=" C   THR C  28 "
            pdb=" CB  THR C  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.41e-01
  chirality pdb=" CA  LEU D  61 "
            pdb=" N   LEU D  61 "
            pdb=" C   LEU D  61 "
            pdb=" CB  LEU D  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  PRO E  32 "
            pdb=" N   PRO E  32 "
            pdb=" C   PRO E  32 "
            pdb=" CB  PRO E  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 1357 not shown)

  Planarity restraints: 1536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  86 "   -0.027 5.00e-02 4.00e+02   4.19e-02 2.80e+00
        pdb=" N   PRO C  87 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO C  87 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  87 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D 121 "    0.008 2.00e-02 2.50e+03   1.62e-02 2.61e+00
        pdb=" C   PRO D 121 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   PRO D 121 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LYS D 122 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  14 "   -0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO B  15 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B  15 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  15 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1533 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 223
        2.69 -     3.24: 8167
        3.24 -     3.79: 13738
        3.79 -     4.35: 17435
        4.35 -     4.90: 29893
  Nonbonded interactions: 69456
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 245 "
            pdb=" OH  TYR B 315 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" OG  SER B 323 "
            pdb=" OG  SER B 326 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" OG1 THR E  73 "
            pdb=" OD2 ASP E  85 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OG  SER B 355 "
            pdb=" OD1 ASP B 357 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NZ  LYS E  91 "
            pdb=" OD2 ASP B  86 "
     model   vdw
     2.219 3.120
  ... (remaining 69451 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:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.760
  Find NCS groups from input model:        0.040
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
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      :  0.004   0.038   8717  Z= 0.159
  Angle     :  0.566   9.729  11893  Z= 0.291
  Chirality :  0.044   0.172   1360
  Planarity :  0.003   0.042   1536
  Dihedral  : 16.209  89.822   2934
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 27.19 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.06 (0.25), residues: 1150
  helix:  1.54 (0.37), residues: 203
  sheet: -1.84 (0.30), residues: 285
  loop : -0.84 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  40 
 TYR   0.008   0.001   TYR C 409 
 PHE   0.011   0.001   PHE C 243 
 TRP   0.008   0.001   TRP B  93 
 HIS   0.005   0.001   HIS C  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8717)
  covalent geometry    : angle       0.56616 (11893)
  hydrogen bonds       : bond        0.19620 (  261)
  hydrogen bonds       : angle       7.88750 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 187
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  189 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7636 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1029
  time to fit residues: 25.2802
Evaluate side-chains
  126 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  189 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 108 ASN
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  65 HIS
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.085690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.065074 restraints weight = 29220.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.067495 restraints weight = 16775.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.069130 restraints weight = 12116.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.070187 restraints weight = 9862.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.070922 restraints weight = 8625.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8717  Z= 0.167
  Angle     :  0.623  12.697  11893  Z= 0.313
  Chirality :  0.045   0.177   1360
  Planarity :  0.004   0.041   1536
  Dihedral  :  4.419  55.762   1249
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 26.80 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.25), residues: 1150
  helix:  1.35 (0.36), residues: 218
  sheet: -1.70 (0.30), residues: 294
  loop : -1.06 (0.24), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  65 
 TYR   0.014   0.001   TYR C  32 
 PHE   0.015   0.001   PHE D  78 
 TRP   0.013   0.001   TRP B 179 
 HIS   0.005   0.001   HIS B 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8717)
  covalent geometry    : angle       0.62349 (11893)
  hydrogen bonds       : bond        0.03811 (  261)
  hydrogen bonds       : angle       5.69637 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  516 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7783 (tp-100)
REVERT: A  576 LYS cc_start: 0.8968 (mttt) cc_final: 0.8536 (tttt)
REVERT: A  685 LYS cc_start: 0.8695 (tmtt) cc_final: 0.8379 (ttmm)
REVERT: D   73 GLU cc_start: 0.8592 (pt0) cc_final: 0.8318 (pt0)
REVERT: D  120 MET cc_start: 0.8693 (mmm) cc_final: 0.8336 (mmm)
REVERT: D  125 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8916 (mm-40)
REVERT: E   95 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8444 (mtp85)
REVERT: C   36 MET cc_start: 0.8447 (ttm) cc_final: 0.8224 (ttt)
REVERT: C  154 TYR cc_start: 0.8931 (p90) cc_final: 0.8637 (p90)
REVERT: C  253 MET cc_start: 0.8425 (mpp) cc_final: 0.7895 (mpp)
REVERT: C  342 LEU cc_start: 0.9401 (tp) cc_final: 0.9138 (tt)
REVERT: C  365 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8169 (mt-10)
REVERT: C  394 SER cc_start: 0.9577 (OUTLIER) cc_final: 0.9260 (t)
REVERT: B   20 ASP cc_start: 0.8672 (t0) cc_final: 0.8179 (t0)
REVERT: B   47 GLU cc_start: 0.8568 (pm20) cc_final: 0.7392 (pm20)
REVERT: B  185 TYR cc_start: 0.9123 (m-10) cc_final: 0.8913 (m-10)
REVERT: B  267 TYR cc_start: 0.9065 (m-80) cc_final: 0.8844 (m-80)
REVERT: B  324 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8331 (mp0)
REVERT: B  369 TYR cc_start: 0.8109 (m-80) cc_final: 0.7670 (m-80)
  outliers start: 34
  outliers final: 11
  residues processed: 170
  average time/residue: 0.0981
  time to fit residues: 22.8227
Evaluate side-chains
  145 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  566 HIS
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  125 GLN
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   95 ARG
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  353 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0770
   chunk 110 optimal weight:    0.0980
   chunk 76 optimal weight:    0.9980
   chunk 111 optimal weight:    4.9990
   chunk 64 optimal weight:    0.3980
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
A 575 ASN
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 108 ASN
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 322 GLN
B  30 HIS
B  40 ASN
B  65 HIS
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.086388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.065189 restraints weight = 29492.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.067856 restraints weight = 15820.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.069652 restraints weight = 11047.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.070831 restraints weight = 8802.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.071506 restraints weight = 7625.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8717  Z= 0.117
  Angle     :  0.606  12.116  11893  Z= 0.299
  Chirality :  0.045   0.176   1360
  Planarity :  0.004   0.076   1536
  Dihedral  :  4.034  19.301   1247
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 28.87 %
    Favored  : 68.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.25), residues: 1150
  helix:  1.50 (0.36), residues: 213
  sheet: -1.67 (0.29), residues: 299
  loop : -1.01 (0.24), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  40 
 TYR   0.011   0.001   TYR B 267 
 PHE   0.013   0.001   PHE C  61 
 TRP   0.011   0.001   TRP C 255 
 HIS   0.003   0.001   HIS B 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8717)
  covalent geometry    : angle       0.60550 (11893)
  hydrogen bonds       : bond        0.03379 (  261)
  hydrogen bonds       : angle       5.24071 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7612 (tp-100)
REVERT: A  576 LYS cc_start: 0.9029 (mttt) cc_final: 0.8538 (tttt)
REVERT: A  685 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8316 (ttmm)
REVERT: A  700 ASP cc_start: 0.7361 (p0) cc_final: 0.7108 (p0)
REVERT: A  704 LEU cc_start: 0.8486 (mt) cc_final: 0.8279 (mt)
REVERT: D   73 GLU cc_start: 0.8716 (pt0) cc_final: 0.8401 (pt0)
REVERT: C   36 MET cc_start: 0.8518 (ttm) cc_final: 0.8243 (ttt)
REVERT: C  253 MET cc_start: 0.8417 (mpp) cc_final: 0.7777 (mpp)
REVERT: C  324 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8736 (mm-40)
REVERT: C  365 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8216 (mt-10)
REVERT: B   10 TRP cc_start: 0.9331 (m100) cc_final: 0.9070 (m100)
REVERT: B   18 SER cc_start: 0.9395 (t) cc_final: 0.9024 (p)
REVERT: B   20 ASP cc_start: 0.8591 (t0) cc_final: 0.8142 (t0)
REVERT: B   40 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8172 (p0)
REVERT: B  173 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7982 (m-80)
REVERT: B  267 TYR cc_start: 0.9041 (m-80) cc_final: 0.8694 (m-80)
REVERT: B  297 TYR cc_start: 0.8780 (m-10) cc_final: 0.8285 (m-10)
REVERT: B  324 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8409 (mt-10)
REVERT: B  369 TYR cc_start: 0.8080 (m-80) cc_final: 0.7725 (m-80)
  outliers start: 22
  outliers final: 9
  residues processed: 166
  average time/residue: 0.0913
  time to fit residues: 21.1049
Evaluate side-chains
  143 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  566 HIS
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain B residue   40 ASN
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 83 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 114 optimal weight:    0.0770
   chunk 68 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:   30.0000
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:   30.0000
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 705 GLN
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 322 GLN
B  30 HIS
B  40 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.086407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.065210 restraints weight = 30123.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.067772 restraints weight = 16622.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.069495 restraints weight = 11794.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.070596 restraints weight = 9527.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.071397 restraints weight = 8307.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8717  Z= 0.118
  Angle     :  0.608  13.469  11893  Z= 0.292
  Chirality :  0.045   0.173   1360
  Planarity :  0.004   0.043   1536
  Dihedral  :  3.902  19.397   1247
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 29.25 %
    Favored  : 67.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.24), residues: 1150
  helix:  1.61 (0.36), residues: 214
  sheet: -1.66 (0.28), residues: 313
  loop : -0.94 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  40 
 TYR   0.011   0.001   TYR C 154 
 PHE   0.019   0.001   PHE A 508 
 TRP   0.010   0.001   TRP C 255 
 HIS   0.004   0.001   HIS B  11 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8717)
  covalent geometry    : angle       0.60769 (11893)
  hydrogen bonds       : bond        0.03077 (  261)
  hydrogen bonds       : angle       4.95685 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7652 (tp-100)
REVERT: A  576 LYS cc_start: 0.9002 (mttt) cc_final: 0.8587 (tttt)
REVERT: A  685 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8341 (ttmm)
REVERT: A  700 ASP cc_start: 0.7393 (p0) cc_final: 0.7040 (p0)
REVERT: A  704 LEU cc_start: 0.8480 (mt) cc_final: 0.8244 (mt)
REVERT: A  705 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8657 (pp30)
REVERT: D   73 GLU cc_start: 0.8731 (pt0) cc_final: 0.8348 (pt0)
REVERT: D  101 VAL cc_start: 0.9782 (p) cc_final: 0.8380 (p)
REVERT: E   53 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8767 (tp30)
REVERT: E  100 PHE cc_start: 0.8856 (m-80) cc_final: 0.8642 (m-80)
REVERT: C  253 MET cc_start: 0.8370 (mpp) cc_final: 0.7830 (mpp)
REVERT: C  365 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8146 (mt-10)
REVERT: C  394 SER cc_start: 0.9665 (OUTLIER) cc_final: 0.9183 (t)
REVERT: B   10 TRP cc_start: 0.9222 (m100) cc_final: 0.8985 (m100)
REVERT: B   14 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8703 (mt-10)
REVERT: B   18 SER cc_start: 0.9322 (t) cc_final: 0.9002 (p)
REVERT: B   20 ASP cc_start: 0.8506 (t0) cc_final: 0.8149 (t0)
REVERT: B  173 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8070 (m-80)
REVERT: B  324 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8329 (mt-10)
REVERT: B  351 ASP cc_start: 0.8414 (t0) cc_final: 0.7830 (m-30)
  outliers start: 25
  outliers final: 11
  residues processed: 159
  average time/residue: 0.0971
  time to fit residues: 21.3567
Evaluate side-chains
  146 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  566 HIS
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  705 GLN
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 31 optimal weight:    0.8980
   chunk 102 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0470
   chunk 23 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
D 108 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 328 HIS
B  30 HIS
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.087033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.067080 restraints weight = 29924.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.069684 restraints weight = 16370.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.071406 restraints weight = 11451.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.072518 restraints weight = 9157.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.073244 restraints weight = 7923.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8717  Z= 0.106
  Angle     :  0.599  12.260  11893  Z= 0.286
  Chirality :  0.044   0.152   1360
  Planarity :  0.004   0.042   1536
  Dihedral  :  3.836  19.320   1247
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 28.09 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.24), residues: 1150
  helix:  1.59 (0.35), residues: 214
  sheet: -1.65 (0.27), residues: 313
  loop : -0.91 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 556 
 TYR   0.009   0.001   TYR B 267 
 PHE   0.022   0.001   PHE A 508 
 TRP   0.010   0.001   TRP C 255 
 HIS   0.003   0.001   HIS B  11 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8717)
  covalent geometry    : angle       0.59874 (11893)
  hydrogen bonds       : bond        0.02853 (  261)
  hydrogen bonds       : angle       4.82407 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7622 (tp-100)
REVERT: A  576 LYS cc_start: 0.9020 (mttt) cc_final: 0.8584 (tttt)
REVERT: A  685 LYS cc_start: 0.8745 (tmtt) cc_final: 0.8393 (ttmm)
REVERT: A  700 ASP cc_start: 0.7326 (p0) cc_final: 0.6978 (p0)
REVERT: A  704 LEU cc_start: 0.8446 (mt) cc_final: 0.8188 (mt)
REVERT: A  705 GLN cc_start: 0.8945 (mt0) cc_final: 0.8411 (mp10)
REVERT: D   73 GLU cc_start: 0.8774 (pt0) cc_final: 0.8494 (pt0)
REVERT: E   53 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8788 (tp30)
REVERT: E   95 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8401 (mtp85)
REVERT: C   15 ARG cc_start: 0.8541 (tpm170) cc_final: 0.8312 (tpm170)
REVERT: C  253 MET cc_start: 0.8405 (mpp) cc_final: 0.7717 (mpp)
REVERT: C  324 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8786 (mm-40)
REVERT: C  365 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8124 (mt-10)
REVERT: C  394 SER cc_start: 0.9685 (OUTLIER) cc_final: 0.9155 (t)
REVERT: C  406 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7860 (tm-30)
REVERT: B   14 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8686 (mt-10)
REVERT: B   18 SER cc_start: 0.9353 (t) cc_final: 0.9037 (p)
REVERT: B   20 ASP cc_start: 0.8507 (t0) cc_final: 0.8138 (t0)
REVERT: B  324 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8283 (mt-10)
REVERT: B  351 ASP cc_start: 0.8420 (t0) cc_final: 0.7855 (m-30)
  outliers start: 30
  outliers final: 18
  residues processed: 157
  average time/residue: 0.0949
  time to fit residues: 20.4225
Evaluate side-chains
  150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  566 HIS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   95 ARG
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 112 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9990
   chunk 69 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0770
   overall best weight:    1.1544

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

Flipped N/Q/H residues before XYZ refinement:
A 705 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
B  65 HIS
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.086018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.065582 restraints weight = 30060.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.068125 restraints weight = 16687.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.069864 restraints weight = 11833.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.071003 restraints weight = 9508.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.071773 restraints weight = 8240.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8717  Z= 0.141
  Angle     :  0.601  12.415  11893  Z= 0.289
  Chirality :  0.044   0.161   1360
  Planarity :  0.004   0.062   1536
  Dihedral  :  3.883  21.514   1247
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 27.96 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.24), residues: 1150
  helix:  1.68 (0.35), residues: 213
  sheet: -1.66 (0.27), residues: 313
  loop : -0.91 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 556 
 TYR   0.010   0.001   TYR C 154 
 PHE   0.016   0.001   PHE A 508 
 TRP   0.011   0.001   TRP A 571 
 HIS   0.009   0.001   HIS C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8717)
  covalent geometry    : angle       0.60109 (11893)
  hydrogen bonds       : bond        0.02842 (  261)
  hydrogen bonds       : angle       4.80269 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7618 (tp-100)
REVERT: A  576 LYS cc_start: 0.9047 (mttt) cc_final: 0.8595 (tttt)
REVERT: A  685 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8405 (ttmm)
REVERT: A  700 ASP cc_start: 0.7314 (p0) cc_final: 0.7087 (p0)
REVERT: D   73 GLU cc_start: 0.8873 (pt0) cc_final: 0.8462 (pt0)
REVERT: E   40 ARG cc_start: 0.8987 (ptt-90) cc_final: 0.8626 (ptt-90)
REVERT: E   53 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8827 (tp30)
REVERT: C  176 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.6766 (m170)
REVERT: C  203 CYS cc_start: 0.8293 (m) cc_final: 0.7935 (m)
REVERT: C  365 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8111 (mt-10)
REVERT: C  394 SER cc_start: 0.9703 (OUTLIER) cc_final: 0.9204 (t)
REVERT: B   14 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8704 (mt-10)
REVERT: B   18 SER cc_start: 0.9366 (t) cc_final: 0.8916 (m)
REVERT: B   20 ASP cc_start: 0.8549 (t0) cc_final: 0.8150 (t0)
REVERT: B   70 ASN cc_start: 0.8661 (m-40) cc_final: 0.8349 (m-40)
REVERT: B  324 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8276 (mt-10)
  outliers start: 32
  outliers final: 21
  residues processed: 148
  average time/residue: 0.1005
  time to fit residues: 20.5994
Evaluate side-chains
  145 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  566 HIS
Chi-restraints excluded: chain A residue  619 ASP
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  705 GLN
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  176 HIS
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 83 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 36 optimal weight:    1.9990
   chunk 111 optimal weight:    7.9990
   chunk 102 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0370
   chunk 87 optimal weight:    8.9990
   chunk 88 optimal weight:    0.1980
   chunk 107 optimal weight:    8.9990
   overall best weight:    1.2062

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

Flipped N/Q/H residues before XYZ refinement:
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
B  65 HIS
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.085217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.065138 restraints weight = 30352.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.067605 restraints weight = 16881.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.069323 restraints weight = 11934.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.070397 restraints weight = 9570.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.071189 restraints weight = 8292.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8717  Z= 0.143
  Angle     :  0.607  11.413  11893  Z= 0.292
  Chirality :  0.044   0.162   1360
  Planarity :  0.004   0.051   1536
  Dihedral  :  3.904  21.244   1247
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 28.74 %
    Favored  : 67.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.24), residues: 1150
  helix:  1.55 (0.35), residues: 219
  sheet: -1.60 (0.27), residues: 311
  loop : -0.88 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 301 
 TYR   0.010   0.001   TYR C 409 
 PHE   0.012   0.001   PHE A 508 
 TRP   0.012   0.001   TRP A 690 
 HIS   0.009   0.001   HIS C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8717)
  covalent geometry    : angle       0.60705 (11893)
  hydrogen bonds       : bond        0.02786 (  261)
  hydrogen bonds       : angle       4.77148 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7547 (tp-100)
REVERT: A  685 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8413 (ttmm)
REVERT: A  705 GLN cc_start: 0.8851 (mt0) cc_final: 0.8522 (mp10)
REVERT: D   73 GLU cc_start: 0.8839 (pt0) cc_final: 0.8457 (pt0)
REVERT: D  101 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9035 (p)
REVERT: D  105 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8472 (mm-30)
REVERT: E   40 ARG cc_start: 0.8983 (ptt-90) cc_final: 0.8636 (ptt-90)
REVERT: E   53 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8827 (tp30)
REVERT: E   95 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8389 (mtp85)
REVERT: E  100 PHE cc_start: 0.8892 (m-80) cc_final: 0.8644 (m-80)
REVERT: C  176 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6772 (m170)
REVERT: C  203 CYS cc_start: 0.8335 (m) cc_final: 0.7955 (m)
REVERT: C  253 MET cc_start: 0.8304 (mpp) cc_final: 0.7546 (mpp)
REVERT: C  365 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8151 (mt-10)
REVERT: C  394 SER cc_start: 0.9727 (OUTLIER) cc_final: 0.9215 (t)
REVERT: C  406 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: B   14 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8697 (mt-10)
REVERT: B   18 SER cc_start: 0.9347 (t) cc_final: 0.8795 (m)
REVERT: B   20 ASP cc_start: 0.8558 (t0) cc_final: 0.8147 (t0)
REVERT: B   70 ASN cc_start: 0.8599 (m-40) cc_final: 0.8039 (t0)
REVERT: B  324 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8277 (mt-10)
REVERT: B  351 ASP cc_start: 0.8329 (t0) cc_final: 0.7681 (m-30)
  outliers start: 29
  outliers final: 20
  residues processed: 145
  average time/residue: 0.1004
  time to fit residues: 20.2161
Evaluate side-chains
  144 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  566 HIS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  619 ASP
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   95 ARG
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  176 HIS
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   chunk 4 optimal weight:   20.0000
   chunk 74 optimal weight:    0.0170
   chunk 50 optimal weight:    4.9990
   chunk 91 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 78 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.7424

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

Flipped N/Q/H residues before XYZ refinement:
D 108 ASN
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
B  65 HIS
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.084217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.063545 restraints weight = 30224.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.066077 restraints weight = 16930.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.067788 restraints weight = 12031.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.068838 restraints weight = 9724.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.069611 restraints weight = 8479.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8717  Z= 0.184
  Angle     :  0.620  11.549  11893  Z= 0.302
  Chirality :  0.045   0.168   1360
  Planarity :  0.004   0.042   1536
  Dihedral  :  3.996  23.287   1247
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 28.61 %
    Favored  : 67.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.24), residues: 1150
  helix:  1.59 (0.36), residues: 220
  sheet: -1.61 (0.27), residues: 321
  loop : -0.84 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 556 
 TYR   0.009   0.001   TYR C 409 
 PHE   0.014   0.001   PHE A 508 
 TRP   0.015   0.002   TRP A 571 
 HIS   0.008   0.001   HIS C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8717)
  covalent geometry    : angle       0.62027 (11893)
  hydrogen bonds       : bond        0.02919 (  261)
  hydrogen bonds       : angle       4.80214 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7511 (tp-100)
REVERT: A  557 MET cc_start: 0.9197 (tmm) cc_final: 0.8958 (tmm)
REVERT: A  616 SER cc_start: 0.8181 (m) cc_final: 0.7973 (p)
REVERT: A  705 GLN cc_start: 0.8912 (mt0) cc_final: 0.8477 (mp10)
REVERT: D   73 GLU cc_start: 0.8791 (pt0) cc_final: 0.8410 (pt0)
REVERT: D  101 VAL cc_start: 0.9496 (OUTLIER) cc_final: 0.9022 (p)
REVERT: D  105 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8558 (mm-30)
REVERT: E   40 ARG cc_start: 0.8937 (ptt-90) cc_final: 0.8572 (ptt-90)
REVERT: E   53 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8826 (tp30)
REVERT: E   95 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8324 (mtp85)
REVERT: E  100 PHE cc_start: 0.8999 (m-80) cc_final: 0.8655 (m-80)
REVERT: C  176 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.6777 (m170)
REVERT: C  203 CYS cc_start: 0.8373 (m) cc_final: 0.7981 (m)
REVERT: C  253 MET cc_start: 0.8369 (mpp) cc_final: 0.7524 (mpp)
REVERT: C  365 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8153 (mt-10)
REVERT: B   18 SER cc_start: 0.9386 (t) cc_final: 0.8856 (m)
REVERT: B   20 ASP cc_start: 0.8594 (t0) cc_final: 0.8135 (t0)
REVERT: B   70 ASN cc_start: 0.8756 (m110) cc_final: 0.8512 (m-40)
REVERT: B  324 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8189 (mp0)
REVERT: B  351 ASP cc_start: 0.8351 (t0) cc_final: 0.7731 (m-30)
  outliers start: 29
  outliers final: 20
  residues processed: 139
  average time/residue: 0.1027
  time to fit residues: 19.8170
Evaluate side-chains
  139 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   95 ARG
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  176 HIS
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 85 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 4 optimal weight:   20.0000
   chunk 90 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
B  40 ASN
B  65 HIS
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.086115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.066860 restraints weight = 29296.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.069317 restraints weight = 15916.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.070986 restraints weight = 11120.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.072128 restraints weight = 8868.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.072800 restraints weight = 7621.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8717  Z= 0.141
  Angle     :  0.623  11.460  11893  Z= 0.300
  Chirality :  0.045   0.161   1360
  Planarity :  0.004   0.042   1536
  Dihedral  :  3.969  22.819   1247
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 28.61 %
    Favored  : 67.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.24), residues: 1150
  helix:  1.55 (0.36), residues: 220
  sheet: -1.60 (0.27), residues: 322
  loop : -0.84 (0.24), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 556 
 TYR   0.009   0.001   TYR C 409 
 PHE   0.012   0.001   PHE A 508 
 TRP   0.010   0.001   TRP A 571 
 HIS   0.008   0.001   HIS C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8717)
  covalent geometry    : angle       0.62342 (11893)
  hydrogen bonds       : bond        0.02844 (  261)
  hydrogen bonds       : angle       4.74534 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 121
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7606 (tp-100)
REVERT: A  556 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7923 (ttp-110)
REVERT: A  685 LYS cc_start: 0.8960 (tmmt) cc_final: 0.8465 (ttmm)
REVERT: A  705 GLN cc_start: 0.8892 (mt0) cc_final: 0.8451 (mp10)
REVERT: D   73 GLU cc_start: 0.8708 (pt0) cc_final: 0.8327 (pt0)
REVERT: D  101 VAL cc_start: 0.9504 (OUTLIER) cc_final: 0.8942 (p)
REVERT: D  105 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8355 (mm-30)
REVERT: E   40 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8509 (ptt-90)
REVERT: E   53 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8699 (tp30)
REVERT: E  100 PHE cc_start: 0.8939 (m-80) cc_final: 0.8690 (m-80)
REVERT: C  176 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.6957 (m170)
REVERT: C  203 CYS cc_start: 0.8122 (m) cc_final: 0.7840 (m)
REVERT: C  253 MET cc_start: 0.8295 (mpp) cc_final: 0.7511 (mpp)
REVERT: C  365 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8089 (mt-10)
REVERT: B   18 SER cc_start: 0.9355 (t) cc_final: 0.8863 (m)
REVERT: B   20 ASP cc_start: 0.8536 (t0) cc_final: 0.8146 (t0)
REVERT: B   70 ASN cc_start: 0.8800 (m110) cc_final: 0.8587 (m-40)
REVERT: B  324 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8256 (mp0)
REVERT: B  351 ASP cc_start: 0.8333 (t0) cc_final: 0.7736 (m-30)
  outliers start: 29
  outliers final: 20
  residues processed: 141
  average time/residue: 0.1045
  time to fit residues: 20.2048
Evaluate side-chains
  142 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  619 ASP
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   40 ARG
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  176 HIS
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  335 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 108 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 96 optimal weight:    0.5980
   chunk 67 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 24 optimal weight:    8.9990
   chunk 80 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
D  39 HIS
D 108 ASN
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
B  65 HIS
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.087492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.067555 restraints weight = 29399.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.070109 restraints weight = 16103.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.071785 restraints weight = 11322.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.072871 restraints weight = 9125.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.073425 restraints weight = 7918.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8717  Z= 0.136
  Angle     :  0.654  17.022  11893  Z= 0.313
  Chirality :  0.045   0.216   1360
  Planarity :  0.004   0.047   1536
  Dihedral  :  3.956  24.082   1247
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 29.12 %
    Favored  : 67.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.25), residues: 1150
  helix:  1.64 (0.36), residues: 220
  sheet: -1.54 (0.27), residues: 322
  loop : -0.79 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 556 
 TYR   0.010   0.001   TYR C 409 
 PHE   0.011   0.001   PHE A 508 
 TRP   0.022   0.001   TRP A 571 
 HIS   0.007   0.001   HIS C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8717)
  covalent geometry    : angle       0.65435 (11893)
  hydrogen bonds       : bond        0.02918 (  261)
  hydrogen bonds       : angle       4.69200 (  729)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7815 (tp-100)
REVERT: A  685 LYS cc_start: 0.8954 (tmmt) cc_final: 0.8663 (tmtt)
REVERT: D   73 GLU cc_start: 0.8676 (pt0) cc_final: 0.8297 (pt0)
REVERT: E   40 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8519 (ptt-90)
REVERT: E   53 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8676 (tp30)
REVERT: E  100 PHE cc_start: 0.8981 (m-80) cc_final: 0.8699 (m-80)
REVERT: C  176 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.6993 (m170)
REVERT: C  203 CYS cc_start: 0.8134 (m) cc_final: 0.7850 (m)
REVERT: C  253 MET cc_start: 0.8298 (mpp) cc_final: 0.7516 (mpp)
REVERT: C  365 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8085 (mt-10)
REVERT: B   18 SER cc_start: 0.9336 (t) cc_final: 0.8840 (m)
REVERT: B   20 ASP cc_start: 0.8554 (t0) cc_final: 0.8139 (t0)
REVERT: B   70 ASN cc_start: 0.8774 (m110) cc_final: 0.8272 (t0)
REVERT: B  299 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: B  324 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8255 (mp0)
REVERT: B  351 ASP cc_start: 0.8341 (t0) cc_final: 0.7744 (m-30)
  outliers start: 24
  outliers final: 20
  residues processed: 136
  average time/residue: 0.1023
  time to fit residues: 19.2096
Evaluate side-chains
  138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  619 ASP
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   40 ARG
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  176 HIS
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  335 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 78 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   chunk 46 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 705 GLN
D  93 GLN
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.086455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.066161 restraints weight = 29441.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.068743 restraints weight = 16451.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.070439 restraints weight = 11672.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.071534 restraints weight = 9435.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.072050 restraints weight = 8215.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.151   8717  Z= 0.210
  Angle     :  0.996  59.200  11893  Z= 0.574
  Chirality :  0.045   0.197   1360
  Planarity :  0.004   0.047   1536
  Dihedral  :  3.947  23.988   1247
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 29.38 %
    Favored  : 67.14 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.25), residues: 1150
  helix:  1.61 (0.36), residues: 220
  sheet: -1.53 (0.27), residues: 322
  loop : -0.79 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 556 
 TYR   0.010   0.001   TYR C 409 
 PHE   0.009   0.001   PHE A 508 
 TRP   0.020   0.001   TRP A 571 
 HIS   0.007   0.001   HIS C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 8717)
  covalent geometry    : angle       0.99608 (11893)
  hydrogen bonds       : bond        0.02992 (  261)
  hydrogen bonds       : angle       4.71327 (  729)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1691.55 seconds
wall clock time: 29 minutes 56.60 seconds (1796.60 seconds total)