Starting phenix.real_space_refine
on Fri May 16 01:00:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iqg_35661/05_2025/8iqg_35661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iqg_35661/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iqg_35661/05_2025/8iqg_35661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iqg_35661/05_2025/8iqg_35661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iqg_35661/05_2025/8iqg_35661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iqg_35661/05_2025/8iqg_35661.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 6}
          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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, '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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP: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: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 19, 'ASP:plan': 13}
          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: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 6, 'ARG:plan': 1, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 105
  Time building chain proxies: 4.94, per 1000 atoms: 0.58
  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: 1.91
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.93
  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: 2.13

  Time building geometry restraints manager: 2.26 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:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.460
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.840
-------------------------------------------------------------------------------
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 : 13.95
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (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
 TRP   0.008   0.001   TRP B  93 
 HIS   0.005   0.001   HIS C  78 
 PHE   0.011   0.001   PHE C 243 
 TYR   0.008   0.001   TYR C 409 
 ARG   0.005   0.000   ARG E  40 

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

*********************** 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  : 0.920 
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: 0.2376
  time to fit residues: 58.3512
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  : 0.889 
-------------------------------------------------------------------------------
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 97 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0370
   chunk 67 optimal weight:    0.0770
   chunk 104 optimal weight:    9.9990
   overall best weight:    0.5616

-------------------------------------------------------------------------------
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  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.087043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.065638 restraints weight = 29152.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.068276 restraints weight = 15994.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.070044 restraints weight = 11279.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8717  Z= 0.126
  Angle     :  0.622  13.114  11893  Z= 0.309
  Chirality :  0.045   0.176   1360
  Planarity :  0.004   0.039   1536
  Dihedral  :  4.387  54.076   1249
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 27.19 %
    Favored  : 68.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.25), residues: 1150
  helix:  1.30 (0.36), residues: 218
  sheet: -1.63 (0.30), residues: 298
  loop : -1.05 (0.24), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 179 
 HIS   0.005   0.001   HIS B 345 
 PHE   0.013   0.001   PHE D  78 
 TYR   0.014   0.001   TYR C  32 
 ARG   0.006   0.001   ARG C  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03660 (  261)
  hydrogen bonds       : angle       5.56485 (  729)
  covalent geometry    : bond        0.00287 ( 8717)
  covalent geometry    : angle       0.62210 (11893)

*********************** 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
  189 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7728 (tp-100)
REVERT: A  576 LYS cc_start: 0.8969 (mttt) cc_final: 0.8577 (tttm)
REVERT: A  685 LYS cc_start: 0.8734 (tmtt) cc_final: 0.8371 (ttmm)
REVERT: A  702 LYS cc_start: 0.9257 (ptmm) cc_final: 0.8492 (ptmm)
REVERT: D   73 GLU cc_start: 0.8664 (pt0) cc_final: 0.8352 (pt0)
REVERT: D   93 GLN cc_start: 0.8812 (tt0) cc_final: 0.8605 (tt0)
REVERT: D  120 MET cc_start: 0.8556 (mmm) cc_final: 0.8351 (mmm)
REVERT: E   95 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8467 (mtp85)
REVERT: C   36 MET cc_start: 0.8424 (ttm) cc_final: 0.8169 (ttt)
REVERT: C  154 TYR cc_start: 0.8975 (p90) cc_final: 0.8676 (p90)
REVERT: C  253 MET cc_start: 0.8417 (mpp) cc_final: 0.7851 (mpp)
REVERT: C  342 LEU cc_start: 0.9391 (tp) cc_final: 0.9128 (tt)
REVERT: C  365 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8205 (mt-10)
REVERT: C  394 SER cc_start: 0.9557 (OUTLIER) cc_final: 0.9153 (t)
REVERT: B   18 SER cc_start: 0.9387 (t) cc_final: 0.8828 (p)
REVERT: B   20 ASP cc_start: 0.8679 (t0) cc_final: 0.8225 (t0)
REVERT: B   40 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8236 (p0)
REVERT: B   47 GLU cc_start: 0.8654 (pm20) cc_final: 0.7337 (pm20)
REVERT: B  185 TYR cc_start: 0.9093 (m-10) cc_final: 0.8842 (m-10)
REVERT: B  189 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7668 (tp)
REVERT: B  267 TYR cc_start: 0.9055 (m-80) cc_final: 0.8691 (m-80)
REVERT: B  324 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8276 (mp0)
REVERT: B  369 TYR cc_start: 0.7986 (m-80) cc_final: 0.7610 (m-80)
  outliers start: 33
  outliers final: 7
  residues processed: 178
  average time/residue: 0.2137
  time to fit residues: 51.6899
Evaluate side-chains
  147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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 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  365 GLU
Chi-restraints excluded: chain C residue  394 SER
Chi-restraints excluded: chain B residue   40 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.083601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.063033 restraints weight = 30377.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.065420 restraints weight = 17212.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.067006 restraints weight = 12361.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   8717  Z= 0.237
  Angle     :  0.632  11.520  11893  Z= 0.316
  Chirality :  0.046   0.178   1360
  Planarity :  0.004   0.055   1536
  Dihedral  :  4.261  37.635   1249
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 26.93 %
    Favored  : 68.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.25), residues: 1150
  helix:  1.47 (0.36), residues: 213
  sheet: -1.64 (0.29), residues: 313
  loop : -0.97 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  42 
 HIS   0.005   0.001   HIS C 226 
 PHE   0.014   0.001   PHE D  78 
 TYR   0.011   0.001   TYR C 409 
 ARG   0.008   0.001   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  261)
  hydrogen bonds       : angle       5.32532 (  729)
  covalent geometry    : bond        0.00527 ( 8717)
  covalent geometry    : angle       0.63178 (11893)

*********************** 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
  160 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7613 (tp-100)
REVERT: A  576 LYS cc_start: 0.9026 (mttt) cc_final: 0.8577 (tttt)
REVERT: A  685 LYS cc_start: 0.8634 (tmtt) cc_final: 0.8295 (ttmm)
REVERT: A  700 ASP cc_start: 0.7412 (p0) cc_final: 0.7160 (p0)
REVERT: D   73 GLU cc_start: 0.8729 (pt0) cc_final: 0.8448 (pt0)
REVERT: D  120 MET cc_start: 0.8715 (mmm) cc_final: 0.8475 (mmm)
REVERT: E   53 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8822 (tp30)
REVERT: C  253 MET cc_start: 0.8366 (mpp) cc_final: 0.7798 (mpp)
REVERT: C  324 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8647 (mm-40)
REVERT: C  342 LEU cc_start: 0.9429 (tp) cc_final: 0.9197 (tt)
REVERT: C  365 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8217 (mt-10)
REVERT: C  394 SER cc_start: 0.9691 (OUTLIER) cc_final: 0.9290 (t)
REVERT: C  399 MET cc_start: 0.8628 (tmm) cc_final: 0.8354 (tmm)
REVERT: B   18 SER cc_start: 0.9362 (t) cc_final: 0.9004 (p)
REVERT: B   20 ASP cc_start: 0.8639 (t0) cc_final: 0.8178 (t0)
REVERT: B  324 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8426 (mt-10)
  outliers start: 32
  outliers final: 16
  residues processed: 148
  average time/residue: 0.2020
  time to fit residues: 40.9040
Evaluate side-chains
  134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain D residue   89 VAL
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   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  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  120 THR
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 27 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0770
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   overall best weight:    0.7540

-------------------------------------------------------------------------------
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  65 HIS
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.085077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.064560 restraints weight = 29797.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.067184 restraints weight = 15737.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.068929 restraints weight = 10910.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8717  Z= 0.126
  Angle     :  0.594  11.601  11893  Z= 0.292
  Chirality :  0.045   0.170   1360
  Planarity :  0.004   0.038   1536
  Dihedral  :  4.010  19.552   1247
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 28.35 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.25), residues: 1150
  helix:  1.55 (0.36), residues: 214
  sheet: -1.69 (0.28), residues: 318
  loop : -0.92 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 255 
 HIS   0.003   0.001   HIS B  11 
 PHE   0.017   0.001   PHE A 508 
 TYR   0.014   0.001   TYR C 154 
 ARG   0.006   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03192 (  261)
  hydrogen bonds       : angle       4.98701 (  729)
  covalent geometry    : bond        0.00293 ( 8717)
  covalent geometry    : angle       0.59439 (11893)

*********************** 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
  168 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7540 (tp-100)
REVERT: A  576 LYS cc_start: 0.9040 (mttt) cc_final: 0.8568 (tttt)
REVERT: A  685 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8300 (ttmm)
REVERT: D   73 GLU cc_start: 0.8744 (pt0) cc_final: 0.8424 (pt0)
REVERT: D  120 MET cc_start: 0.8639 (mmm) cc_final: 0.8430 (mmm)
REVERT: E   40 ARG cc_start: 0.9084 (ptt-90) cc_final: 0.8760 (ptt-90)
REVERT: E   53 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8674 (tp30)
REVERT: E   78 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7772 (mtm180)
REVERT: E   95 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8362 (mtp85)
REVERT: C  253 MET cc_start: 0.8454 (mpp) cc_final: 0.7817 (mpp)
REVERT: C  324 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8888 (mm-40)
REVERT: C  342 LEU cc_start: 0.9384 (tp) cc_final: 0.9098 (tt)
REVERT: C  365 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8219 (mt-10)
REVERT: B   14 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8720 (mt-10)
REVERT: B   18 SER cc_start: 0.9376 (t) cc_final: 0.9028 (p)
REVERT: B   20 ASP cc_start: 0.8623 (t0) cc_final: 0.8223 (t0)
REVERT: B  324 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8367 (mt-10)
REVERT: B  351 ASP cc_start: 0.8341 (t0) cc_final: 0.7758 (m-30)
  outliers start: 27
  outliers final: 14
  residues processed: 155
  average time/residue: 0.2065
  time to fit residues: 43.8351
Evaluate side-chains
  142 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
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 D residue   92 LEU
Chi-restraints excluded: chain E residue   30 THR
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   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 B residue  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  189 LEU
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 100 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 74 optimal weight:    0.8980
   chunk 107 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 705 GLN
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
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.085184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.064648 restraints weight = 29817.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.067174 restraints weight = 16716.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.068841 restraints weight = 11916.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8717  Z= 0.126
  Angle     :  0.584  11.725  11893  Z= 0.285
  Chirality :  0.045   0.161   1360
  Planarity :  0.004   0.035   1536
  Dihedral  :  3.933  19.722   1247
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 27.32 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.25), residues: 1150
  helix:  1.66 (0.36), residues: 213
  sheet: -1.65 (0.28), residues: 318
  loop : -0.87 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 255 
 HIS   0.009   0.001   HIS C 176 
 PHE   0.011   0.001   PHE D  78 
 TYR   0.009   0.001   TYR B 267 
 ARG   0.007   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02985 (  261)
  hydrogen bonds       : angle       4.82342 (  729)
  covalent geometry    : bond        0.00293 ( 8717)
  covalent geometry    : angle       0.58415 (11893)

*********************** 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
  168 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7588 (tp-100)
REVERT: A  685 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8385 (ttmm)
REVERT: D   73 GLU cc_start: 0.8767 (pt0) cc_final: 0.8436 (pt0)
REVERT: E   40 ARG cc_start: 0.8993 (ptt-90) cc_final: 0.8709 (ptp-170)
REVERT: E   53 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8670 (tp30)
REVERT: E  100 PHE cc_start: 0.8951 (m-80) cc_final: 0.8673 (m-80)
REVERT: C  203 CYS cc_start: 0.8416 (m) cc_final: 0.8070 (m)
REVERT: C  253 MET cc_start: 0.8383 (mpp) cc_final: 0.7656 (mpp)
REVERT: C  324 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8856 (mm-40)
REVERT: C  365 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8153 (mt-10)
REVERT: C  406 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7918 (tm-30)
REVERT: B   14 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8727 (mt-10)
REVERT: B   18 SER cc_start: 0.9335 (t) cc_final: 0.8883 (m)
REVERT: B   20 ASP cc_start: 0.8597 (t0) cc_final: 0.8204 (t0)
REVERT: B   70 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8159 (m-40)
REVERT: B  324 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: B  351 ASP cc_start: 0.8343 (t0) cc_final: 0.7786 (m-30)
  outliers start: 35
  outliers final: 21
  residues processed: 155
  average time/residue: 0.2174
  time to fit residues: 46.0357
Evaluate side-chains
  144 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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 A residue  705 GLN
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   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  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   70 ASN
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  189 LEU
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 29 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 88 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 13 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 705 GLN
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  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.085236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.064853 restraints weight = 29677.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.067486 restraints weight = 15764.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.069274 restraints weight = 10883.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8717  Z= 0.118
  Angle     :  0.611  14.975  11893  Z= 0.291
  Chirality :  0.045   0.157   1360
  Planarity :  0.004   0.035   1536
  Dihedral  :  3.890  19.451   1247
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.24), residues: 1150
  helix:  1.69 (0.36), residues: 214
  sheet: -1.64 (0.27), residues: 318
  loop : -0.88 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 402 
 HIS   0.011   0.001   HIS C 176 
 PHE   0.025   0.001   PHE A 508 
 TYR   0.015   0.001   TYR C 154 
 ARG   0.008   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02930 (  261)
  hydrogen bonds       : angle       4.76411 (  729)
  covalent geometry    : bond        0.00278 ( 8717)
  covalent geometry    : angle       0.61115 (11893)

*********************** 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
  163 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7522 (tp-100)
REVERT: A  685 LYS cc_start: 0.8731 (tmtt) cc_final: 0.8379 (ttmm)
REVERT: D   73 GLU cc_start: 0.8796 (pt0) cc_final: 0.8564 (pt0)
REVERT: E   40 ARG cc_start: 0.9003 (ptt-90) cc_final: 0.8735 (ptp-170)
REVERT: E   53 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8636 (tp30)
REVERT: E   95 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8377 (mtp85)
REVERT: E  100 PHE cc_start: 0.8980 (m-80) cc_final: 0.8674 (m-80)
REVERT: C   15 ARG cc_start: 0.8695 (tpm170) cc_final: 0.8483 (tpm170)
REVERT: C  203 CYS cc_start: 0.8494 (m) cc_final: 0.8225 (m)
REVERT: C  324 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8829 (mm-40)
REVERT: C  365 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8191 (mt-10)
REVERT: B   14 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8715 (mt-10)
REVERT: B   18 SER cc_start: 0.9349 (t) cc_final: 0.8866 (m)
REVERT: B   20 ASP cc_start: 0.8632 (t0) cc_final: 0.8195 (t0)
REVERT: B   70 ASN cc_start: 0.8818 (m110) cc_final: 0.8470 (m-40)
REVERT: B  324 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8314 (mt-10)
  outliers start: 30
  outliers final: 20
  residues processed: 150
  average time/residue: 0.2065
  time to fit residues: 42.4259
Evaluate side-chains
  141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  554 PHE
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  701 LEU
Chi-restraints excluded: chain A residue  705 GLN
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain E residue   30 THR
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  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  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  189 LEU
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 87 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 109 optimal weight:    3.9990
   chunk 112 optimal weight:    9.9990
   chunk 101 optimal weight:    0.5980
   chunk 34 optimal weight:    5.9990
   chunk 88 optimal weight:    0.2980
   chunk 42 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 705 GLN
** 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  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 322 GLN
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 = 0.3586 r_free = 0.3586 target = 0.082948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.062166 restraints weight = 30042.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.064622 restraints weight = 17112.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.066255 restraints weight = 12292.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8717  Z= 0.234
  Angle     :  0.638  11.436  11893  Z= 0.314
  Chirality :  0.046   0.176   1360
  Planarity :  0.004   0.034   1536
  Dihedral  :  4.050  19.726   1247
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 28.61 %
    Favored  : 67.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.25), residues: 1150
  helix:  1.53 (0.36), residues: 219
  sheet: -1.62 (0.27), residues: 322
  loop : -0.94 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 402 
 HIS   0.012   0.001   HIS C 176 
 PHE   0.028   0.002   PHE A 508 
 TYR   0.014   0.001   TYR C 154 
 ARG   0.007   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03140 (  261)
  hydrogen bonds       : angle       4.91512 (  729)
  covalent geometry    : bond        0.00518 ( 8717)
  covalent geometry    : angle       0.63750 (11893)

*********************** 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
  154 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7520 (tp-100)
REVERT: D   73 GLU cc_start: 0.8803 (pt0) cc_final: 0.8449 (pt0)
REVERT: E   40 ARG cc_start: 0.8990 (ptt-90) cc_final: 0.8744 (ptp-170)
REVERT: E   53 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8688 (tp30)
REVERT: E   95 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8319 (mtp85)
REVERT: E  100 PHE cc_start: 0.9042 (m-80) cc_final: 0.8720 (m-80)
REVERT: C  253 MET cc_start: 0.8387 (mpp) cc_final: 0.7565 (mpp)
REVERT: C  324 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8800 (mm-40)
REVERT: C  365 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8210 (mt-10)
REVERT: B   18 SER cc_start: 0.9356 (t) cc_final: 0.8842 (m)
REVERT: B   20 ASP cc_start: 0.8656 (t0) cc_final: 0.8213 (t0)
REVERT: B   70 ASN cc_start: 0.8994 (m110) cc_final: 0.8518 (m-40)
REVERT: B  324 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8336 (mt-10)
REVERT: B  351 ASP cc_start: 0.8338 (t0) cc_final: 0.7730 (m-30)
  outliers start: 33
  outliers final: 21
  residues processed: 142
  average time/residue: 0.2151
  time to fit residues: 41.9146
Evaluate side-chains
  136 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  554 PHE
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain E residue   30 THR
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  269 VAL
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  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  335 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 575 ASN
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 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 = 0.3695 r_free = 0.3695 target = 0.086497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.066732 restraints weight = 29815.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.069280 restraints weight = 16004.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.071011 restraints weight = 11131.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8717  Z= 0.125
  Angle     :  0.624  11.799  11893  Z= 0.301
  Chirality :  0.045   0.160   1360
  Planarity :  0.004   0.035   1536
  Dihedral  :  3.970  19.839   1247
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.64 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.24), residues: 1150
  helix:  1.55 (0.36), residues: 220
  sheet: -1.56 (0.27), residues: 323
  loop : -0.91 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 402 
 HIS   0.016   0.001   HIS C 176 
 PHE   0.032   0.001   PHE A 508 
 TYR   0.013   0.001   TYR C 154 
 ARG   0.009   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02993 (  261)
  hydrogen bonds       : angle       4.75589 (  729)
  covalent geometry    : bond        0.00294 ( 8717)
  covalent geometry    : angle       0.62391 (11893)

*********************** 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
  156 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7522 (tp-100)
REVERT: A  575 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8246 (m-40)
REVERT: A  685 LYS cc_start: 0.8909 (tmmt) cc_final: 0.8461 (ttmm)
REVERT: D   73 GLU cc_start: 0.8750 (pt0) cc_final: 0.8366 (pt0)
REVERT: D  105 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8425 (mm-30)
REVERT: E   53 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8556 (tp30)
REVERT: E   95 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8276 (mtp85)
REVERT: E  100 PHE cc_start: 0.8996 (m-80) cc_final: 0.8696 (m-80)
REVERT: C  253 MET cc_start: 0.8298 (mpp) cc_final: 0.7485 (mpp)
REVERT: C  324 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8826 (mm-40)
REVERT: C  365 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8117 (mt-10)
REVERT: B   18 SER cc_start: 0.9313 (t) cc_final: 0.8884 (m)
REVERT: B   20 ASP cc_start: 0.8565 (t0) cc_final: 0.8201 (t0)
REVERT: B   45 LYS cc_start: 0.9124 (mtpp) cc_final: 0.8513 (mtmt)
REVERT: B   70 ASN cc_start: 0.8814 (m110) cc_final: 0.8438 (m-40)
REVERT: B  229 HIS cc_start: 0.8563 (m-70) cc_final: 0.8150 (m-70)
REVERT: B  351 ASP cc_start: 0.8395 (t0) cc_final: 0.7769 (m-30)
  outliers start: 31
  outliers final: 19
  residues processed: 145
  average time/residue: 0.2246
  time to fit residues: 44.0655
Evaluate side-chains
  143 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  554 PHE
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  575 ASN
Chi-restraints excluded: chain A residue  619 ASP
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain E residue   30 THR
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  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  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  189 LEU
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 79 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0060
   chunk 33 optimal weight:    0.3980
   chunk 105 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.6800

-------------------------------------------------------------------------------
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**
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.085796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.065700 restraints weight = 29735.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.068224 restraints weight = 16346.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.069866 restraints weight = 11546.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8717  Z= 0.120
  Angle     :  0.641  11.878  11893  Z= 0.308
  Chirality :  0.046   0.173   1360
  Planarity :  0.004   0.042   1536
  Dihedral  :  3.955  19.770   1247
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 29.64 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.24), residues: 1150
  helix:  1.72 (0.36), residues: 214
  sheet: -1.50 (0.28), residues: 308
  loop : -0.87 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 571 
 HIS   0.014   0.001   HIS C 176 
 PHE   0.042   0.001   PHE A 508 
 TYR   0.012   0.001   TYR C 154 
 ARG   0.009   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02911 (  261)
  hydrogen bonds       : angle       4.75441 (  729)
  covalent geometry    : bond        0.00284 ( 8717)
  covalent geometry    : angle       0.64075 (11893)

*********************** 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
  151 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7518 (tp-100)
REVERT: A  685 LYS cc_start: 0.8967 (tmmt) cc_final: 0.8424 (ttmm)
REVERT: D    5 GLN cc_start: 0.6796 (pm20) cc_final: 0.5603 (pm20)
REVERT: D   73 GLU cc_start: 0.8716 (pt0) cc_final: 0.8347 (pt0)
REVERT: D   93 GLN cc_start: 0.8618 (tt0) cc_final: 0.8365 (tt0)
REVERT: E   53 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8517 (tp30)
REVERT: E  100 PHE cc_start: 0.8972 (m-80) cc_final: 0.8713 (m-80)
REVERT: C  253 MET cc_start: 0.8301 (mpp) cc_final: 0.7534 (mpp)
REVERT: C  352 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7681 (tp30)
REVERT: C  365 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8099 (mt-10)
REVERT: B   18 SER cc_start: 0.9271 (t) cc_final: 0.8875 (m)
REVERT: B   20 ASP cc_start: 0.8531 (t0) cc_final: 0.8188 (t0)
REVERT: B   70 ASN cc_start: 0.8824 (m110) cc_final: 0.8427 (m-40)
REVERT: B  229 HIS cc_start: 0.8564 (m-70) cc_final: 0.8180 (m-70)
REVERT: B  299 GLU cc_start: 0.8741 (tp30) cc_final: 0.8496 (tm-30)
REVERT: B  351 ASP cc_start: 0.8309 (t0) cc_final: 0.7729 (m-30)
  outliers start: 26
  outliers final: 20
  residues processed: 143
  average time/residue: 0.2004
  time to fit residues: 39.9081
Evaluate side-chains
  138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  554 PHE
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 A residue  701 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain E residue   30 THR
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  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  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  189 LEU
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 96 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   chunk 21 optimal weight:    0.1980
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D  39 HIS
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.087579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.066517 restraints weight = 29448.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.069156 restraints weight = 16142.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.070870 restraints weight = 11406.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8717  Z= 0.120
  Angle     :  0.662  12.169  11893  Z= 0.318
  Chirality :  0.046   0.238   1360
  Planarity :  0.004   0.048   1536
  Dihedral  :  3.983  19.721   1247
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 30.15 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.24), residues: 1150
  helix:  1.71 (0.36), residues: 215
  sheet: -1.43 (0.27), residues: 322
  loop : -0.91 (0.24), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 571 
 HIS   0.013   0.001   HIS C 176 
 PHE   0.052   0.001   PHE A 508 
 TYR   0.011   0.001   TYR C 154 
 ARG   0.009   0.001   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02991 (  261)
  hydrogen bonds       : angle       4.73688 (  729)
  covalent geometry    : bond        0.00283 ( 8717)
  covalent geometry    : angle       0.66168 (11893)

********************** 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
  147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7490 (tp-100)
REVERT: A  685 LYS cc_start: 0.8971 (tmmt) cc_final: 0.8572 (tmtt)
REVERT: D   73 GLU cc_start: 0.8730 (pt0) cc_final: 0.8356 (pt0)
REVERT: E   36 ARG cc_start: 0.9047 (ptp-170) cc_final: 0.8408 (ptp90)
REVERT: E   53 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8506 (tp30)
REVERT: E  100 PHE cc_start: 0.9039 (m-80) cc_final: 0.8724 (m-80)
REVERT: C  253 MET cc_start: 0.8331 (mpp) cc_final: 0.7529 (mpp)
REVERT: C  324 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8743 (mm110)
REVERT: C  365 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8154 (mt-10)
REVERT: B   14 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8704 (mt-10)
REVERT: B   18 SER cc_start: 0.9278 (t) cc_final: 0.8851 (m)
REVERT: B   20 ASP cc_start: 0.8604 (t0) cc_final: 0.8219 (t0)
REVERT: B   70 ASN cc_start: 0.8823 (m110) cc_final: 0.8321 (m-40)
REVERT: B   86 ASP cc_start: 0.8523 (t0) cc_final: 0.8117 (m-30)
REVERT: B  229 HIS cc_start: 0.8607 (m-70) cc_final: 0.8197 (m-70)
REVERT: B  299 GLU cc_start: 0.8842 (tp30) cc_final: 0.8577 (tm-30)
REVERT: B  351 ASP cc_start: 0.8335 (t0) cc_final: 0.7728 (m-30)
  outliers start: 22
  outliers final: 20
  residues processed: 141
  average time/residue: 0.2167
  time to fit residues: 41.6913
Evaluate side-chains
  144 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue  701 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   45 ARG
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  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  152 THR
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  296 VAL
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 106 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   chunk 21 optimal weight:    0.1980
   chunk 17 optimal weight:   40.0000
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** E  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 122 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.087216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.065729 restraints weight = 29790.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.068356 restraints weight = 16317.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.070105 restraints weight = 11578.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8717  Z= 0.125
  Angle     :  0.659  12.425  11893  Z= 0.317
  Chirality :  0.046   0.232   1360
  Planarity :  0.004   0.066   1536
  Dihedral  :  3.989  25.073   1247
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 30.41 %
    Favored  : 66.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.24), residues: 1150
  helix:  1.76 (0.36), residues: 215
  sheet: -1.26 (0.28), residues: 317
  loop : -0.92 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 571 
 HIS   0.012   0.001   HIS C 176 
 PHE   0.062   0.001   PHE A 508 
 TYR   0.011   0.001   TYR C 154 
 ARG   0.013   0.001   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03010 (  261)
  hydrogen bonds       : angle       4.73329 (  729)
  covalent geometry    : bond        0.00292 ( 8717)
  covalent geometry    : angle       0.65856 (11893)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2934.06 seconds
wall clock time: 52 minutes 8.99 seconds (3128.99 seconds total)